4-105121535-C-T

Variant names:

• chr4-105121535-C-T
• rs1859161

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 0.949 in 152,352 control chromosomes in the GnomAD database, including 68,708 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 0.95 (68708 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.308
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.978 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: 0.949 AC: 144502 AN: 152234 Hom.: 68644 Cov.: 33

Gnomad AFR AF: 0.986

Gnomad AMI AF: 0.973

Gnomad AMR AF: 0.942

Gnomad ASJ AF: 0.947

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.970

Gnomad FIN AF: 0.967

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.920

Gnomad OTH AF: 0.936

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

GnomAD4 genome AF: 0.949 AC: 144625 AN: 152352 Hom.: 68708 Cov.: 33 AF XY: 0.953 AC XY: 70965 AN XY: 74490

African (AFR) AF: 0.986 AC: 41002 AN: 41582

American (AMR) AF: 0.943 AC: 14426 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.947 AC: 3288 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5188 AN: 5190

South Asian (SAS) AF: 0.971 AC: 4682 AN: 4822

European-Finnish (FIN) AF: 0.967 AC: 10269 AN: 10622

Middle Eastern (MID) AF: 0.942 AC: 277 AN: 294

European-Non Finnish (NFE) AF: 0.920 AC: 62622 AN: 68036

Other (OTH) AF: 0.938 AC: 1984 AN: 2116

Alfa AF: 0.931 Hom.: 150967

Bravo AF: 0.948

Asia WGS AF: 0.986 AC: 3428 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.63
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs1859161; hg19: chr4-106042692;