4-110748064-T-C

Position:

• chr4-110748064-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 0.694 in 151,566 control chromosomes in the GnomAD database, including 37,944 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 (37944 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.434

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.798 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: 0.694 AC: 105074 AN: 151448 Hom.: 37927 Cov.: 31

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.928

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.809

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.803

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.694 AC: 105120 AN: 151566 Hom.: 37944 Cov.: 31 AF XY: 0.683 AC XY: 50573 AN XY: 74098

Gnomad4 AFR AF: 0.583

Gnomad4 AMR AF: 0.594

Gnomad4 ASJ AF: 0.616

Gnomad4 EAS AF: 0.262

Gnomad4 SAS AF: 0.631

Gnomad4 FIN AF: 0.809

Gnomad4 NFE AF: 0.803

Gnomad4 OTH AF: 0.701

Alfa AF: 0.713 Hom.: 7388

Bravo AF: 0.673

Asia WGS AF: 0.468 AC: 1630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.65
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2634071; hg19: chr4-111669220;