4-145563710-G-A

Variant names:

• chr4-145563710-G-A
• rs2036138

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 0.36 in 152,082 control chromosomes in the GnomAD database, including 11,885 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 0.36 (11885 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.475
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.495 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: 0.361 AC: 54791 AN: 151964 Hom.: 11884 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.360 AC: 54800 AN: 152082 Hom.: 11885 Cov.: 32 AF XY: 0.356 AC XY: 26504 AN XY: 74358

African (AFR) AF: 0.151 AC: 6253 AN: 41492

American (AMR) AF: 0.295 AC: 4509 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 1139 AN: 3470

East Asian (EAS) AF: 0.126 AC: 653 AN: 5174

South Asian (SAS) AF: 0.346 AC: 1667 AN: 4816

European-Finnish (FIN) AF: 0.509 AC: 5388 AN: 10580

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.500 AC: 33961 AN: 67952

Other (OTH) AF: 0.352 AC: 741 AN: 2104

Alfa AF: 0.395 Hom.: 2269

Bravo AF: 0.334

Asia WGS AF: 0.251 AC: 876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.9
DANN	Benign	0.59
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs2036138; hg19: chr4-146484862;