7-44376473-G-C

Variant names:

• chr7-44376473-G-C
• rs6960920

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 0.38 in 152,012 control chromosomes in the GnomAD database, including 11,432 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 0.38 (11432 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.838
• Publications: 5 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 (EAS) allele frequency at 95% confidence interval = 0.521 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: 0.380 AC: 57670 AN: 151894 Hom.: 11419 Cov.: 32

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.380 AC: 57694 AN: 152012 Hom.: 11432 Cov.: 32 AF XY: 0.385 AC XY: 28592 AN XY: 74300

African (AFR) AF: 0.271 AC: 11238 AN: 41450

American (AMR) AF: 0.495 AC: 7564 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1007 AN: 3470

East Asian (EAS) AF: 0.538 AC: 2776 AN: 5160

South Asian (SAS) AF: 0.460 AC: 2212 AN: 4812

European-Finnish (FIN) AF: 0.413 AC: 4366 AN: 10574

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.400 AC: 27208 AN: 67954

Other (OTH) AF: 0.395 AC: 833 AN: 2110

Alfa AF: 0.391 Hom.: 1501

Bravo AF: 0.381

Asia WGS AF: 0.502 AC: 1748 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	5.7
DANN	Benign	0.64
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs6960920; hg19: chr7-44416072;