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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.178

Gnomad4 AMR AF: 0.0621

Gnomad4 ASJ AF: 0.0493

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0622

Gnomad4 FIN AF: 0.0572

Gnomad4 NFE AF: 0.0712

Gnomad4 OTH AF: 0.0894

Alfa AF: 0.0447 Hom.: 55

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28631020; hg19: chr6-67653279;