4-65718188-T-C

Position:

• chr4-65718188-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 0.69 in 151,626 control chromosomes in the GnomAD database, including 38,021 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 0.69 (38021 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.278

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.874 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.690 AC: 104578 AN: 151508 Hom.: 38026 Cov.: 31

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.899

Gnomad AMR AF: 0.767

Gnomad ASJ AF: 0.711

Gnomad EAS AF: 0.895

Gnomad SAS AF: 0.781

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.784

Gnomad OTH AF: 0.711

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

GnomAD4 genome AF: 0.690 AC: 104603 AN: 151626 Hom.: 38021 Cov.: 31 AF XY: 0.695 AC XY: 51487 AN XY: 74086

Gnomad4 AFR AF: 0.436

Gnomad4 AMR AF: 0.767

Gnomad4 ASJ AF: 0.711

Gnomad4 EAS AF: 0.896

Gnomad4 SAS AF: 0.782

Gnomad4 FIN AF: 0.797

Gnomad4 NFE AF: 0.784

Gnomad4 OTH AF: 0.711

Alfa AF: 0.771 Hom.: 89608

Bravo AF: 0.676

Asia WGS AF: 0.804 AC: 2794 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.6
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4629506; hg19: chr4-66583906;