4-186572661-T-C

Position:

• chr4-186572661-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.369 in 151,980 control chromosomes in the GnomAD database, including 10,836 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 0.37 (10836 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.119

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.369 AC: 56018 AN: 151864 Hom.: 10820 Cov.: 32

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.369 AC: 56051 AN: 151980 Hom.: 10836 Cov.: 32 AF XY: 0.377 AC XY: 28025 AN XY: 74294

Gnomad4 AFR AF: 0.289

Gnomad4 AMR AF: 0.461

Gnomad4 ASJ AF: 0.336

Gnomad4 EAS AF: 0.478

Gnomad4 SAS AF: 0.557

Gnomad4 FIN AF: 0.424

Gnomad4 NFE AF: 0.370

Gnomad4 OTH AF: 0.379

Alfa AF: 0.365 Hom.: 3435

Bravo AF: 0.361

Asia WGS AF: 0.497 AC: 1729 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	1.6
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10030173; hg19: chr4-187493815;