4-41709845-T-C

Variant names:

• chr4-41709845-T-C
• rs6823379

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 0.143 in 152,220 control chromosomes in the GnomAD database, including 2,887 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 (2887 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.771
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.348 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: 0.142 AC: 21661 AN: 152102 Hom.: 2867 Cov.: 32

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.0909

Gnomad ASJ AF: 0.0589

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.0700

Gnomad FIN AF: 0.0319

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0559

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.143 AC: 21724 AN: 152220 Hom.: 2887 Cov.: 32 AF XY: 0.141 AC XY: 10480 AN XY: 74434

African (AFR) AF: 0.352 AC: 14621 AN: 41496

American (AMR) AF: 0.0908 AC: 1388 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0589 AC: 204 AN: 3466

East Asian (EAS) AF: 0.132 AC: 685 AN: 5184

South Asian (SAS) AF: 0.0700 AC: 338 AN: 4826

European-Finnish (FIN) AF: 0.0319 AC: 339 AN: 10616

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0559 AC: 3801 AN: 68020

Other (OTH) AF: 0.109 AC: 230 AN: 2112

Alfa AF: 0.112 Hom.: 542

Bravo AF: 0.155

Asia WGS AF: 0.116 AC: 401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.7
DANN	Benign	0.74
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs6823379; hg19: chr4-41711862;