4-71735614-T-C

Variant names:

• chr4-71735614-T-C
• rs12512631

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 0.351 in 152,028 control chromosomes in the GnomAD database, including 9,424 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 0.35 (9424 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.664

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.409 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: 0.351 AC: 53267 AN: 151912 Hom.: 9424 Cov.: 32

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.351 AC: 53296 AN: 152028 Hom.: 9424 Cov.: 32 AF XY: 0.352 AC XY: 26128 AN XY: 74332

Gnomad4 AFR AF: 0.345

Gnomad4 AMR AF: 0.417

Gnomad4 ASJ AF: 0.424

Gnomad4 EAS AF: 0.210

Gnomad4 SAS AF: 0.259

Gnomad4 FIN AF: 0.373

Gnomad4 NFE AF: 0.348

Gnomad4 OTH AF: 0.365

Alfa AF: 0.353 Hom.: 19452

Bravo AF: 0.355

Asia WGS AF: 0.275 AC: 954 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.7
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12512631; hg19: chr4-72601331;