chr4-110705611-A-C

Variant names:

• chr4-110705611-A-C
• rs2595099

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 0.642 in 151,856 control chromosomes in the GnomAD database, including 31,637 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 0.64 (31637 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.655

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.672 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: 0.642 AC: 97363 AN: 151738 Hom.: 31615 Cov.: 31

Gnomad AFR AF: 0.657

Gnomad AMI AF: 0.775

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.642 AC: 97441 AN: 151856 Hom.: 31637 Cov.: 31 AF XY: 0.629 AC XY: 46667 AN XY: 74226

Gnomad4 AFR AF: 0.657

Gnomad4 AMR AF: 0.604

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.412

Gnomad4 SAS AF: 0.568

Gnomad4 FIN AF: 0.587

Gnomad4 NFE AF: 0.677

Gnomad4 OTH AF: 0.634

Alfa AF: 0.531 Hom.: 1506

Bravo AF: 0.645

Asia WGS AF: 0.484 AC: 1685 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2595099; hg19: chr4-111626767;