4-110844159-G-C

Variant names:

• chr4-110844159-G-C
• rs6838901

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 0.135 in 152,146 control chromosomes in the GnomAD database, including 1,493 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 0.14 (1493 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.126
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.203 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: 0.136 AC: 20617 AN: 152028 Hom.: 1494 Cov.: 32

Gnomad AFR AF: 0.0977

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.0955

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.135 AC: 20609 AN: 152146 Hom.: 1493 Cov.: 32 AF XY: 0.134 AC XY: 9979 AN XY: 74364

African (AFR) AF: 0.0975 AC: 4048 AN: 41516

American (AMR) AF: 0.0953 AC: 1458 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 510 AN: 3468

East Asian (EAS) AF: 0.213 AC: 1100 AN: 5158

South Asian (SAS) AF: 0.185 AC: 889 AN: 4818

European-Finnish (FIN) AF: 0.147 AC: 1555 AN: 10580

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10673 AN: 67996

Other (OTH) AF: 0.137 AC: 289 AN: 2110

Alfa AF: 0.150 Hom.: 212

Bravo AF: 0.130

Asia WGS AF: 0.169 AC: 588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.0
DANN	Benign	0.64
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs6838901; hg19: chr4-111765315;