chr4-65894110-C-T

Position:

• chr4-65894110-C-T

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 0.493 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.251

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.65894110C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.578

Gnomad4 AMR AF: 0.457

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.464

Gnomad4 SAS AF: 0.451

Gnomad4 FIN AF: 0.452

Gnomad4 NFE AF: 0.465

Gnomad4 OTH AF: 0.477

Alfa AF: 0.451 Hom.: 12459

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10517949; hg19: chr4-66759828;