rs1885486

Variant names:

• chr6-7695740-G-A
• rs1885486
• ENST00000773040.1:n.332-2247G>A

Variant summary

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

The ENST00000773040.1(ENSG00000300630):​n.332-2247G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 151,556 control chromosomes in the GnomAD database, including 12,599 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 (12599 hom., cov: 30)
• Consequence: ENSG00000300630 ENST00000773040.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.203
• Publications: 16 publications found

Genes affected

ENSG00000300630 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000773040.1. 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
	ENSG00000300630	ENST00000773040.1		n.332-2247G>A		intron	N/A
	ENSG00000300630	ENST00000773041.1		n.76-2247G>A		intron	N/A
	ENSG00000300630	ENST00000773042.1		n.124-2247G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60303 AN: 151438 Hom.: 12597 Cov.: 30

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.398 AC: 60328 AN: 151556 Hom.: 12599 Cov.: 30 AF XY: 0.395 AC XY: 29247 AN XY: 74028

African (AFR) AF: 0.288 AC: 11872 AN: 41284

American (AMR) AF: 0.311 AC: 4741 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.414 AC: 1435 AN: 3470

East Asian (EAS) AF: 0.238 AC: 1226 AN: 5146

South Asian (SAS) AF: 0.552 AC: 2655 AN: 4812

European-Finnish (FIN) AF: 0.470 AC: 4893 AN: 10400

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.472 AC: 32083 AN: 67904

Other (OTH) AF: 0.377 AC: 794 AN: 2104

Alfa AF: 0.436 Hom.: 22277

Bravo AF: 0.376

Asia WGS AF: 0.347 AC: 1206 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.6
DANN	Benign	0.79
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs1885486; hg19: chr6-7695973; COSMIC: COSV67970796;