rs696990

Variant names:

• chr6-70312523-T-C
• rs696990

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 0.252 in 152,002 control chromosomes in the GnomAD database, including 5,421 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 0.25 (5421 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.702
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.367 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: 0.252 AC: 38226 AN: 151884 Hom.: 5398 Cov.: 32

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.298

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.252 AC: 38291 AN: 152002 Hom.: 5421 Cov.: 32 AF XY: 0.250 AC XY: 18603 AN XY: 74288

African (AFR) AF: 0.372 AC: 15430 AN: 41444

American (AMR) AF: 0.213 AC: 3250 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.228 AC: 790 AN: 3468

East Asian (EAS) AF: 0.123 AC: 638 AN: 5168

South Asian (SAS) AF: 0.326 AC: 1573 AN: 4820

European-Finnish (FIN) AF: 0.172 AC: 1824 AN: 10574

Middle Eastern (MID) AF: 0.283 AC: 82 AN: 290

European-Non Finnish (NFE) AF: 0.205 AC: 13926 AN: 67966

Other (OTH) AF: 0.258 AC: 545 AN: 2114

Alfa AF: 0.225 Hom.: 2188

Bravo AF: 0.255

Asia WGS AF: 0.259 AC: 903 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.3
DANN	Benign	0.32
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs696990; hg19: chr6-71022226;