4-110767596-T-C

Variant names:

• chr4-110767596-T-C
• rs2723334

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 0.654 in 152,108 control chromosomes in the GnomAD database, including 34,134 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 0.65 (34134 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0900
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.766 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.655 AC: 99486 AN: 151990 Hom.: 34128 Cov.: 32

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.923

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.770

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.772

Gnomad OTH AF: 0.667

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

GnomAD4 genome AF: 0.654 AC: 99518 AN: 152108 Hom.: 34134 Cov.: 32 AF XY: 0.642 AC XY: 47776 AN XY: 74362

African (AFR) AF: 0.513 AC: 21283 AN: 41480

American (AMR) AF: 0.572 AC: 8749 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.609 AC: 2113 AN: 3470

East Asian (EAS) AF: 0.264 AC: 1365 AN: 5164

South Asian (SAS) AF: 0.607 AC: 2925 AN: 4818

European-Finnish (FIN) AF: 0.770 AC: 8152 AN: 10588

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.772 AC: 52482 AN: 67982

Other (OTH) AF: 0.667 AC: 1408 AN: 2112

Alfa AF: 0.719 Hom.: 51893

Bravo AF: 0.635

Asia WGS AF: 0.458 AC: 1597 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	13
DANN	Benign	0.57
PhyloP100		0.090

Splicing

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

Other links and lift over

dbSNP: rs2723334; hg19: chr4-111688752;