rs6841061

Variant names:

• chr4-185078389-G-A
• rs6841061
• ENST00000509017.6:n.1499+6316G>A

Your query was ambiguous. Multiple possible variants found:

• chr4-185078389-G-A
• chr4-185078389-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000826339.1(ENSG00000307445):​n.954C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 518,070 control chromosomes in the GnomAD database, including 97,392 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.63 (30631 hom., cov: 33)
  • Exomes 𝑓: 0.60 (66761 hom.)
• Consequence: ENSG00000307445 ENST00000826339.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.423
• Publications: 5 publications found

Genes affected

LINC02436 (HGNC:53368): (long intergenic non-protein coding RNA 2436)

ENSG00000307445 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000826339.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02436	NR_147059.2		n.1359+6316G>A		intron	N/A
	LINC02436	NR_174102.1		n.989+6316G>A		intron	N/A
	LINC02436	NR_174103.1		n.320-7395G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02436	ENST00000509017.6	TSL:1	n.1499+6316G>A		intron	N/A
	ENSG00000307445	ENST00000826339.1		n.954C>T		non_coding_transcript_exon	Exon 2 of 3
	LINC02436	ENST00000652785.1		n.394-7395G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.630 AC: 95744 AN: 152012 Hom.: 30601 Cov.: 33

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.776

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.753

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.567

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.648

GnomAD2 exomes AF: 0.589 AC: 134859 AN: 228804 AF XY: 0.593

Gnomad AFR exome AF: 0.691

Gnomad AMR exome AF: 0.524

Gnomad ASJ exome AF: 0.745

Gnomad EAS exome AF: 0.333

Gnomad FIN exome AF: 0.566

Gnomad NFE exome AF: 0.630

Gnomad OTH exome AF: 0.613

GnomAD4 exome AF: 0.598 AC: 218973 AN: 365940 Hom.: 66761 Cov.: 0 AF XY: 0.599 AC XY: 125683 AN XY: 209812

African (AFR) AF: 0.693 AC: 7258 AN: 10478

American (AMR) AF: 0.521 AC: 18891 AN: 36228

Ashkenazi Jewish (ASJ) AF: 0.745 AC: 8731 AN: 11712

East Asian (EAS) AF: 0.331 AC: 4351 AN: 13164

South Asian (SAS) AF: 0.576 AC: 38350 AN: 66568

European-Finnish (FIN) AF: 0.565 AC: 9532 AN: 16864

Middle Eastern (MID) AF: 0.705 AC: 2010 AN: 2850

European-Non Finnish (NFE) AF: 0.624 AC: 119588 AN: 191502

Other (OTH) AF: 0.619 AC: 10262 AN: 16574

GnomAD4 genome AF: 0.630 AC: 95822 AN: 152130 Hom.: 30631 Cov.: 33 AF XY: 0.623 AC XY: 46319 AN XY: 74358

African (AFR) AF: 0.691 AC: 28672 AN: 41518

American (AMR) AF: 0.580 AC: 8860 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.753 AC: 2613 AN: 3470

East Asian (EAS) AF: 0.350 AC: 1812 AN: 5174

South Asian (SAS) AF: 0.568 AC: 2741 AN: 4824

European-Finnish (FIN) AF: 0.567 AC: 5981 AN: 10552

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.630 AC: 42865 AN: 67988

Other (OTH) AF: 0.646 AC: 1366 AN: 2114

Alfa AF: 0.629 Hom.: 25551

Bravo AF: 0.634

Asia WGS AF: 0.477 AC: 1661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.45
DANN	Benign	0.60
PhyloP100		-0.42

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6841061; hg19: chr4-185999543;