rs3857481

Variant names:

• chr6-86414851-G-A
• rs3857481

Your query was ambiguous. Multiple possible variants found:

• chr6-86414851-G-A
• chr6-86414851-G-T

Variant summary

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

The variant allele was found at a frequency of 0.287 in 152,064 control chromosomes in the GnomAD database, including 6,400 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 0.29 (6400 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.498
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.287 AC: 43551 AN: 151946 Hom.: 6394 Cov.: 33

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.287 AC: 43576 AN: 152064 Hom.: 6400 Cov.: 33 AF XY: 0.286 AC XY: 21293 AN XY: 74322

African (AFR) AF: 0.228 AC: 9470 AN: 41470

American (AMR) AF: 0.316 AC: 4826 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 859 AN: 3470

East Asian (EAS) AF: 0.263 AC: 1356 AN: 5154

South Asian (SAS) AF: 0.337 AC: 1627 AN: 4824

European-Finnish (FIN) AF: 0.304 AC: 3215 AN: 10578

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.313 AC: 21268 AN: 67972

Other (OTH) AF: 0.256 AC: 540 AN: 2112

Alfa AF: 0.298 Hom.: 17306

Bravo AF: 0.286

Asia WGS AF: 0.269 AC: 933 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.24
DANN	Benign	0.50
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs3857481; hg19: chr6-87124569; COSMIC: COSV69411654;