4-65894110-C-T

Variant names:

• chr4-65894110-C-T
• rs10517949

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 0.493 in 151,928 control chromosomes in the GnomAD database, including 18,784 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 0.49 (18784 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.251
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.572 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: 0.493 AC: 74844 AN: 151810 Hom.: 18771 Cov.: 32

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.493 AC: 74903 AN: 151928 Hom.: 18784 Cov.: 32 AF XY: 0.491 AC XY: 36465 AN XY: 74260

African (AFR) AF: 0.578 AC: 23953 AN: 41424

American (AMR) AF: 0.457 AC: 6976 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1339 AN: 3468

East Asian (EAS) AF: 0.464 AC: 2386 AN: 5146

South Asian (SAS) AF: 0.451 AC: 2172 AN: 4812

European-Finnish (FIN) AF: 0.452 AC: 4770 AN: 10558

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.465 AC: 31601 AN: 67942

Other (OTH) AF: 0.477 AC: 1006 AN: 2108

Alfa AF: 0.459 Hom.: 18532

Bravo AF: 0.494

Asia WGS AF: 0.411 AC: 1432 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.8
DANN	Benign	0.79
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs10517949; hg19: chr4-66759828;