rs28631020

Positions:

• 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.60

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.66943386G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;