4-10147204-T-C

Position:

• chr4-10147204-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 0.435 in 152,046 control chromosomes in the GnomAD database, including 14,621 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 0.43 (14621 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.588

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66096 AN: 151928 Hom.: 14622 Cov.: 33

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.435 AC: 66118 AN: 152046 Hom.: 14621 Cov.: 33 AF XY: 0.437 AC XY: 32439 AN XY: 74316

Gnomad4 AFR AF: 0.420

Gnomad4 AMR AF: 0.366

Gnomad4 ASJ AF: 0.323

Gnomad4 EAS AF: 0.518

Gnomad4 SAS AF: 0.528

Gnomad4 FIN AF: 0.488

Gnomad4 NFE AF: 0.445

Gnomad4 OTH AF: 0.434

Alfa AF: 0.425 Hom.: 23081

Bravo AF: 0.421

Asia WGS AF: 0.529 AC: 1840 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	2.2
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6813385; hg19: chr4-10148828;