7-152677049-C-G

Variant names:

• chr7-152677049-C-G
• rs3218374

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 0.621 in 151,994 control chromosomes in the GnomAD database, including 30,926 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 0.62 (30926 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.886
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.827 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: 0.621 AC: 94238 AN: 151874 Hom.: 30879 Cov.: 32

Gnomad AFR AF: 0.834

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.574

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.618

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.608

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

GnomAD4 genome AF: 0.621 AC: 94345 AN: 151994 Hom.: 30926 Cov.: 32 AF XY: 0.614 AC XY: 45623 AN XY: 74274

African (AFR) AF: 0.834 AC: 34594 AN: 41480

American (AMR) AF: 0.616 AC: 9387 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.597 AC: 2073 AN: 3472

East Asian (EAS) AF: 0.574 AC: 2972 AN: 5182

South Asian (SAS) AF: 0.643 AC: 3095 AN: 4816

European-Finnish (FIN) AF: 0.387 AC: 4078 AN: 10536

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.535 AC: 36360 AN: 67954

Other (OTH) AF: 0.610 AC: 1287 AN: 2110

Alfa AF: 0.582 Hom.: 3315

Bravo AF: 0.645

Asia WGS AF: 0.629 AC: 2186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.58
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs3218374; hg19: chr7-152374134;