chr4-136721193-T-C

Variant names:

• chr4-136721193-T-C
• rs1460133

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 0.106 in 152,200 control chromosomes in the GnomAD database, including 978 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 0.11 (978 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.143 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: 0.106 AC: 16115 AN: 152082 Hom.: 977 Cov.: 32

Gnomad AFR AF: 0.0612

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.0961

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.0154

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.106 AC: 16117 AN: 152200 Hom.: 978 Cov.: 32 AF XY: 0.109 AC XY: 8075 AN XY: 74402

African (AFR) AF: 0.0613 AC: 2545 AN: 41532

American (AMR) AF: 0.0961 AC: 1469 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 594 AN: 3468

East Asian (EAS) AF: 0.0155 AC: 80 AN: 5170

South Asian (SAS) AF: 0.152 AC: 732 AN: 4824

European-Finnish (FIN) AF: 0.161 AC: 1703 AN: 10596

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8575 AN: 67998

Other (OTH) AF: 0.108 AC: 228 AN: 2116

Alfa AF: 0.112 Hom.: 194

Bravo AF: 0.0956

Asia WGS AF: 0.0610 AC: 213 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.9
DANN	Benign	0.50
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs1460133; hg19: chr4-137642348;