chr4-110199557-G-A

Variant names:

• chr4-110199557-G-A
• rs6824447

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 0.541 in 151,924 control chromosomes in the GnomAD database, including 23,432 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 0.54 (23432 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.717 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: 0.541 AC: 82139 AN: 151808 Hom.: 23399 Cov.: 30

Gnomad AFR AF: 0.724

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.490

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.541 AC: 82229 AN: 151924 Hom.: 23432 Cov.: 30 AF XY: 0.536 AC XY: 39772 AN XY: 74238

African (AFR) AF: 0.724 AC: 29991 AN: 41440

American (AMR) AF: 0.453 AC: 6913 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.618 AC: 2146 AN: 3470

East Asian (EAS) AF: 0.338 AC: 1745 AN: 5164

South Asian (SAS) AF: 0.419 AC: 2011 AN: 4800

European-Finnish (FIN) AF: 0.415 AC: 4387 AN: 10564

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.490 AC: 33291 AN: 67928

Other (OTH) AF: 0.530 AC: 1116 AN: 2106

Alfa AF: 0.510 Hom.: 23540

Bravo AF: 0.550

Asia WGS AF: 0.437 AC: 1519 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.86
DANN	Benign	0.29
PhyloP100		-1.3
PromoterAI		-0.0062	Neutral

Splicing

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

Other links and lift over

dbSNP: rs6824447; hg19: chr4-111120713;