rs6685886

Variant names:

• chr1-207320873-C-A
• rs6685886
• ENST00000740658.1:n.116+813G>T

Your query was ambiguous. Multiple possible variants found:

• chr1-207320873-C-A
• chr1-207320873-C-G

Variant summary

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

The ENST00000740658.1(ENSG00000296591):​n.116+813G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 144,118 control chromosomes in the GnomAD database, including 11,748 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 0.40 (11748 hom., cov: 28)
• Consequence: ENSG00000296591 ENST00000740658.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.406
• Publications: 4 publications found

Genes affected

ENSG00000296591 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985251	XR_007066837.1	n.444+813G>T		intron_variant	Intron 1 of 3
LOC107985251	XR_007066838.1	n.444+813G>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296591	ENST00000740658.1	n.116+813G>T		intron_variant	Intron 1 of 2
ENSG00000296591	ENST00000740659.1	n.96+813G>T		intron_variant	Intron 1 of 4
ENSG00000296591	ENST00000740660.1	n.89+813G>T		intron_variant	Intron 1 of 3
ENSG00000296591	ENST00000740661.1	n.86+813G>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.404 AC: 58155 AN: 144056 Hom.: 11738 Cov.: 28

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.542

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.404 AC: 58175 AN: 144118 Hom.: 11748 Cov.: 28 AF XY: 0.404 AC XY: 28371 AN XY: 70142

African (AFR) AF: 0.320 AC: 11669 AN: 36486

American (AMR) AF: 0.450 AC: 6640 AN: 14748

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1700 AN: 3422

East Asian (EAS) AF: 0.371 AC: 1850 AN: 4992

South Asian (SAS) AF: 0.391 AC: 1835 AN: 4694

European-Finnish (FIN) AF: 0.458 AC: 4464 AN: 9754

Middle Eastern (MID) AF: 0.539 AC: 153 AN: 284

European-Non Finnish (NFE) AF: 0.427 AC: 28547 AN: 66838

Other (OTH) AF: 0.450 AC: 903 AN: 2008

Alfa AF: 0.395 Hom.: 1731

Bravo AF: 0.385

Asia WGS AF: 0.332 AC: 1151 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	4.3
DANN	Benign	0.66
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs6685886; hg19: chr1-207494218;