rs28631020

Variant names:

• chr6-66943386-G-A
• rs28631020

Your query was ambiguous. Multiple possible variants found:

• chr6-66943386-G-A
• chr6-66943386-G-C
• chr6-66943386-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 0.0966 in 152,046 control chromosomes in the GnomAD database, including 909 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 0.097 (909 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.60
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.175 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: 0.0964 AC: 14653 AN: 151928 Hom.: 905 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.233

Gnomad AMR AF: 0.0622

Gnomad ASJ AF: 0.0493

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0620

Gnomad FIN AF: 0.0572

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0712

Gnomad OTH AF: 0.0903

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

GnomAD4 genome AF: 0.0966 AC: 14681 AN: 152046 Hom.: 909 Cov.: 32 AF XY: 0.0951 AC XY: 7071 AN XY: 74336

African (AFR) AF: 0.178 AC: 7386 AN: 41442

American (AMR) AF: 0.0621 AC: 949 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0493 AC: 171 AN: 3470

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5160

South Asian (SAS) AF: 0.0622 AC: 300 AN: 4820

European-Finnish (FIN) AF: 0.0572 AC: 605 AN: 10572

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0712 AC: 4841 AN: 67978

Other (OTH) AF: 0.0894 AC: 189 AN: 2114

Alfa AF: 0.0852 Hom.: 556

Bravo AF: 0.0996

Asia WGS AF: 0.0520 AC: 183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.43
DANN	Benign	0.51
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs28631020; hg19: chr6-67653279;