rs675209

Variant names:

• chr6-7101851-T-C
• rs675209

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 0.632 in 151,736 control chromosomes in the GnomAD database, including 31,933 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 0.63 (31933 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.544
• Publications: 56 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.726 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: 0.632 AC: 95770 AN: 151618 Hom.: 31908 Cov.: 29

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.842

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.711

Gnomad EAS AF: 0.0777

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.731

Gnomad OTH AF: 0.670

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

GnomAD4 genome AF: 0.632 AC: 95846 AN: 151736 Hom.: 31933 Cov.: 29 AF XY: 0.624 AC XY: 46225 AN XY: 74124

African (AFR) AF: 0.550 AC: 22711 AN: 41314

American (AMR) AF: 0.607 AC: 9246 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.711 AC: 2468 AN: 3472

East Asian (EAS) AF: 0.0781 AC: 403 AN: 5162

South Asian (SAS) AF: 0.400 AC: 1922 AN: 4800

European-Finnish (FIN) AF: 0.671 AC: 7057 AN: 10518

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.731 AC: 49653 AN: 67916

Other (OTH) AF: 0.661 AC: 1394 AN: 2110

Alfa AF: 0.684 Hom.: 140318

Bravo AF: 0.623

Asia WGS AF: 0.265 AC: 926 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.0
DANN	Benign	0.47
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs675209; hg19: chr6-7102084;