chr4-170037692-C-G

Variant names:

• chr4-170037692-C-G
• rs7657455

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 0.404 in 151,982 control chromosomes in the GnomAD database, including 12,848 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 0.40 (12848 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.188
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.7 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: 0.404 AC: 61368 AN: 151862 Hom.: 12842 Cov.: 32

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.720

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.404 AC: 61407 AN: 151982 Hom.: 12848 Cov.: 32 AF XY: 0.403 AC XY: 29928 AN XY: 74270

African (AFR) AF: 0.319 AC: 13221 AN: 41456

American (AMR) AF: 0.452 AC: 6908 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1457 AN: 3470

East Asian (EAS) AF: 0.720 AC: 3711 AN: 5156

South Asian (SAS) AF: 0.406 AC: 1956 AN: 4818

European-Finnish (FIN) AF: 0.372 AC: 3923 AN: 10544

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.423 AC: 28758 AN: 67948

Other (OTH) AF: 0.446 AC: 943 AN: 2116

Alfa AF: 0.229 Hom.: 473

Bravo AF: 0.411

Asia WGS AF: 0.571 AC: 1980 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.0
DANN	Benign	0.46
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs7657455; hg19: chr4-170958843;