rs1853639

Variant names:

• chr6-86897124-G-A
• rs1853639
• ENST00000468100.1:n.7G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-86897124-G-A
• chr6-86897124-G-C

Variant summary

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

The ENST00000468100.1(ENSG00000217769):​n.7G>A 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 0.629 in 1,594,678 control chromosomes in the GnomAD database, including 316,515 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 0.64 (31098 hom., cov: 32)
  • Exomes 𝑓: 0.63 (285417 hom.)
• Consequence: ENSG00000217769 ENST00000468100.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.30
• Publications: 7 publications found

Genes affected

ENSG00000217769 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.674 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000468100.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000217769	ENST00000468100.1	TSL:6	n.7G>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000301924	ENST00000782918.1		n.155+40562C>T		intron	N/A
	ENSG00000301924	ENST00000782919.1		n.383+31657C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.639 AC: 96991 AN: 151904 Hom.: 31051 Cov.: 32

Gnomad AFR AF: 0.629

Gnomad AMI AF: 0.807

Gnomad AMR AF: 0.685

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.615

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.613

GnomAD4 exome AF: 0.628 AC: 906466 AN: 1442656 Hom.: 285417 Cov.: 33 AF XY: 0.627 AC XY: 450253 AN XY: 718194

African (AFR) AF: 0.627 AC: 20953 AN: 33408

American (AMR) AF: 0.720 AC: 32173 AN: 44686

Ashkenazi Jewish (ASJ) AF: 0.641 AC: 16732 AN: 26108

East Asian (EAS) AF: 0.553 AC: 21952 AN: 39668

South Asian (SAS) AF: 0.588 AC: 50670 AN: 86146

European-Finnish (FIN) AF: 0.659 AC: 25130 AN: 38142

Middle Eastern (MID) AF: 0.587 AC: 2866 AN: 4882

European-Non Finnish (NFE) AF: 0.629 AC: 698416 AN: 1109512

Other (OTH) AF: 0.625 AC: 37574 AN: 60104

GnomAD4 genome AF: 0.639 AC: 97095 AN: 152022 Hom.: 31098 Cov.: 32 AF XY: 0.641 AC XY: 47582 AN XY: 74286

African (AFR) AF: 0.629 AC: 26096 AN: 41470

American (AMR) AF: 0.685 AC: 10478 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.654 AC: 2268 AN: 3470

East Asian (EAS) AF: 0.580 AC: 2989 AN: 5156

South Asian (SAS) AF: 0.573 AC: 2764 AN: 4822

European-Finnish (FIN) AF: 0.663 AC: 6987 AN: 10544

Middle Eastern (MID) AF: 0.623 AC: 182 AN: 292

European-Non Finnish (NFE) AF: 0.637 AC: 43315 AN: 67958

Other (OTH) AF: 0.608 AC: 1282 AN: 2110

Alfa AF: 0.640 Hom.: 4007

Bravo AF: 0.638

Asia WGS AF: 0.591 AC: 2052 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.4
DANN	Benign	0.62
PhyloP100		-2.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1853639;

hg19: chr6-87606842;