chr1-95680412-A-G

Variant names:

• chr1-95680412-A-G
• rs6693882
• ENST00000456933.1:n.308-96735A>G

Variant summary

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

The ENST00000456933.1(LINC02607):​n.308-96735A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 152,102 control chromosomes in the GnomAD database, including 13,266 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 0.38 (13266 hom., cov: 32)
• Consequence: LINC02607 ENST00000456933.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.163
• Publications: 12 publications found

Genes affected

LINC02607 (HGNC:54049): (long intergenic non-protein coding RNA 2607)

LOC101928219 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000456933.1. 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
	LINC02607	ENST00000456933.1	TSL:3	n.308-96735A>G		intron	N/A
	LINC02607	ENST00000664663.1		n.133+54847A>G		intron	N/A
	LINC02607	ENST00000665349.1		n.160+54768A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.376 AC: 57072 AN: 151984 Hom.: 13270 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.392

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.375 AC: 57066 AN: 152102 Hom.: 13266 Cov.: 32 AF XY: 0.373 AC XY: 27694 AN XY: 74344

African (AFR) AF: 0.111 AC: 4624 AN: 41550

American (AMR) AF: 0.360 AC: 5492 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.460 AC: 1597 AN: 3468

East Asian (EAS) AF: 0.233 AC: 1205 AN: 5166

South Asian (SAS) AF: 0.539 AC: 2594 AN: 4816

European-Finnish (FIN) AF: 0.471 AC: 4974 AN: 10562

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.520 AC: 35317 AN: 67958

Other (OTH) AF: 0.395 AC: 833 AN: 2108

Alfa AF: 0.455 Hom.: 53851

Bravo AF: 0.351

Asia WGS AF: 0.361 AC: 1258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.7
DANN	Benign	0.39
PhyloP100		0.16

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: rs6693882;

hg19: chr1-96145968;