rs3857454

Variant names:

• chr6-79399816-G-A
• rs3857454

Your query was ambiguous. Multiple possible variants found:

• chr6-79399816-G-A
• chr6-79399816-G-C

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 0.0858 in 152,242 control chromosomes in the GnomAD database, including 612 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 0.086 (612 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.21
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.118 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: 0.0859 AC: 13065 AN: 152124 Hom.: 612 Cov.: 32

Gnomad AFR AF: 0.0470

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0907

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.0521

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.0858 AC: 13062 AN: 152242 Hom.: 612 Cov.: 32 AF XY: 0.0839 AC XY: 6246 AN XY: 74436

African (AFR) AF: 0.0469 AC: 1951 AN: 41560

American (AMR) AF: 0.0906 AC: 1385 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 571 AN: 3472

East Asian (EAS) AF: 0.101 AC: 521 AN: 5172

South Asian (SAS) AF: 0.127 AC: 611 AN: 4830

European-Finnish (FIN) AF: 0.0521 AC: 552 AN: 10598

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.106 AC: 7195 AN: 68000

Other (OTH) AF: 0.110 AC: 232 AN: 2116

Alfa AF: 0.0964 Hom.: 123

Bravo AF: 0.0863

Asia WGS AF: 0.108 AC: 378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	14
DANN	Benign	0.70
PhyloP100		2.2

Splicing

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

Other links and lift over

dbSNP: rs3857454; hg19: chr6-80109533;