rs6944602

Variant names:

• chr7-50406053-G-A
• rs6944602

Your query was ambiguous. Multiple possible variants found:

• chr7-50406053-G-A
• chr7-50406053-G-T

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 0.151 in 152,130 control chromosomes in the GnomAD database, including 2,031 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 0.15 (2031 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 22 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.191 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: 0.151 AC: 22992 AN: 152012 Hom.: 2034 Cov.: 32

Gnomad AFR AF: 0.0712

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.0393

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.151 AC: 22998 AN: 152130 Hom.: 2031 Cov.: 32 AF XY: 0.151 AC XY: 11217 AN XY: 74384

African (AFR) AF: 0.0712 AC: 2956 AN: 41510

American (AMR) AF: 0.189 AC: 2887 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 592 AN: 3470

East Asian (EAS) AF: 0.0392 AC: 203 AN: 5180

South Asian (SAS) AF: 0.192 AC: 922 AN: 4814

European-Finnish (FIN) AF: 0.147 AC: 1558 AN: 10584

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.194 AC: 13196 AN: 67986

Other (OTH) AF: 0.174 AC: 366 AN: 2106

Alfa AF: 0.164 Hom.: 1282

Bravo AF: 0.151

Asia WGS AF: 0.110 AC: 382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.011
DANN	Benign	0.66
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs6944602; hg19: chr7-50473751;