rs2857211

Positions:

• chr6-32772665-A-G
• chr6-32772665-A-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 0.692 in 152,008 control chromosomes in the GnomAD database, including 36,609 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 0.69 (36609 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00800

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.32772665A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.692 AC: 105090 AN: 151890 Hom.: 36587 Cov.: 32

Gnomad AFR AF: 0.682

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.686

Gnomad ASJ AF: 0.672

Gnomad EAS AF: 0.774

Gnomad SAS AF: 0.890

Gnomad FIN AF: 0.749

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.670

Gnomad OTH AF: 0.691

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

GnomAD4 genome AF: 0.692 AC: 105158 AN: 152008 Hom.: 36609 Cov.: 32 AF XY: 0.700 AC XY: 52018 AN XY: 74298

Gnomad4 AFR AF: 0.682

Gnomad4 AMR AF: 0.686

Gnomad4 ASJ AF: 0.672

Gnomad4 EAS AF: 0.774

Gnomad4 SAS AF: 0.890

Gnomad4 FIN AF: 0.749

Gnomad4 NFE AF: 0.670

Gnomad4 OTH AF: 0.694

Alfa AF: 0.673 Hom.: 23377

Bravo AF: 0.680

Asia WGS AF: 0.830 AC: 2885 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.7
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2857211; hg19: chr6-32740442; COSMIC: COSV54964679;