chr5-148817174-T-C

Variant names:

• chr5-148817174-T-C
• rs877741

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 0.352 in 152,022 control chromosomes in the GnomAD database, including 12,601 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 0.35 (12601 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.554
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.759 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: 0.352 AC: 53468 AN: 151904 Hom.: 12562 Cov.: 32

Gnomad AFR AF: 0.612

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.779

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.352 AC: 53565 AN: 152022 Hom.: 12601 Cov.: 32 AF XY: 0.353 AC XY: 26242 AN XY: 74318

African (AFR) AF: 0.612 AC: 25350 AN: 41414

American (AMR) AF: 0.381 AC: 5814 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 723 AN: 3470

East Asian (EAS) AF: 0.779 AC: 4033 AN: 5176

South Asian (SAS) AF: 0.388 AC: 1870 AN: 4820

European-Finnish (FIN) AF: 0.182 AC: 1926 AN: 10590

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.189 AC: 12831 AN: 67984

Other (OTH) AF: 0.324 AC: 685 AN: 2112

Alfa AF: 0.247 Hom.: 25402

Bravo AF: 0.384

Asia WGS AF: 0.576 AC: 2002 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.7
DANN	Benign	0.52
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs877741; hg19: chr5-148196737;