rs3218373

Variant names:

• chr7-152677078-C-A
• rs3218373

Your query was ambiguous. Multiple possible variants found:

• chr7-152677078-C-A
• chr7-152677078-C-G
• chr7-152677078-C-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 0.149 in 152,086 control chromosomes in the GnomAD database, including 2,126 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 (2126 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0590
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.287 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: 0.149 AC: 22598 AN: 151968 Hom.: 2116 Cov.: 32

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.0361

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.0913

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.149 AC: 22638 AN: 152086 Hom.: 2126 Cov.: 32 AF XY: 0.149 AC XY: 11097 AN XY: 74344

African (AFR) AF: 0.210 AC: 8711 AN: 41480

American (AMR) AF: 0.252 AC: 3840 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 587 AN: 3472

East Asian (EAS) AF: 0.299 AC: 1546 AN: 5170

South Asian (SAS) AF: 0.164 AC: 789 AN: 4818

European-Finnish (FIN) AF: 0.0361 AC: 382 AN: 10586

Middle Eastern (MID) AF: 0.120 AC: 35 AN: 292

European-Non Finnish (NFE) AF: 0.0913 AC: 6209 AN: 67990

Other (OTH) AF: 0.167 AC: 351 AN: 2106

Alfa AF: 0.119 Hom.: 5225

Bravo AF: 0.171

Asia WGS AF: 0.254 AC: 882 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.42
PhyloP100		-0.059

Splicing

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

Other links and lift over

dbSNP: rs3218373; hg19: chr7-152374163;