rs1157128

Variant names:

• chr4-160443991-G-T
• rs1157128

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 0.0792 in 152,128 control chromosomes in the GnomAD database, including 1,275 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 0.079 (1275 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.194
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.236 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: 0.0792 AC: 12037 AN: 152010 Hom.: 1277 Cov.: 32

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0619

Gnomad ASJ AF: 0.00923

Gnomad EAS AF: 0.0593

Gnomad SAS AF: 0.0139

Gnomad FIN AF: 0.0242

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00492

Gnomad OTH AF: 0.0716

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

GnomAD4 genome AF: 0.0792 AC: 12052 AN: 152128 Hom.: 1275 Cov.: 32 AF XY: 0.0783 AC XY: 5827 AN XY: 74382

African (AFR) AF: 0.240 AC: 9941 AN: 41460

American (AMR) AF: 0.0620 AC: 946 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.00923 AC: 32 AN: 3468

East Asian (EAS) AF: 0.0596 AC: 308 AN: 5166

South Asian (SAS) AF: 0.0137 AC: 66 AN: 4828

European-Finnish (FIN) AF: 0.0242 AC: 257 AN: 10604

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.00490 AC: 333 AN: 68014

Other (OTH) AF: 0.0718 AC: 152 AN: 2116

Alfa AF: 0.0294 Hom.: 1414

Bravo AF: 0.0898

Asia WGS AF: 0.0620 AC: 215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	6.4
DANN	Benign	0.85
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs1157128; hg19: chr4-161365143;