4-10147204-T-C

Variant names:

• chr4-10147204-T-C
• rs6813385

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 0.435 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
• Publications: 3 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 (SAS) allele frequency at 95% confidence interval = 0.511 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: 0.435 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

African (AFR) AF: 0.420 AC: 17432 AN: 41460

American (AMR) AF: 0.366 AC: 5591 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1121 AN: 3472

East Asian (EAS) AF: 0.518 AC: 2677 AN: 5168

South Asian (SAS) AF: 0.528 AC: 2545 AN: 4816

European-Finnish (FIN) AF: 0.488 AC: 5160 AN: 10584

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.445 AC: 30242 AN: 67962

Other (OTH) AF: 0.434 AC: 915 AN: 2110

Alfa AF: 0.430 Hom.: 34892

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
PhyloP100		0.59

Splicing

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

Other links and lift over

dbSNP: rs6813385; hg19: chr4-10148828;