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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000740658.1. 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
	ENSG00000296591	ENST00000740658.1		n.116+813G>T		intron	N/A
	ENSG00000296591	ENST00000740659.1		n.96+813G>T		intron	N/A
	ENSG00000296591	ENST00000740660.1		n.89+813G>T		intron	N/A

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 v4.9

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

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

Other links and lift over

dbSNP: rs6685886;

hg19: chr1-207494218;