5-127642416-T-C

Variant names:

• chr5-127642416-T-C
• rs11241936

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 0.398 in 151,148 control chromosomes in the GnomAD database, including 14,477 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 0.40 (14477 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.549
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.671 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: 0.398 AC: 60088 AN: 151036 Hom.: 14455 Cov.: 30

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.0738

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.398 AC: 60151 AN: 151148 Hom.: 14477 Cov.: 30 AF XY: 0.388 AC XY: 28663 AN XY: 73802

African (AFR) AF: 0.677 AC: 27833 AN: 41098

American (AMR) AF: 0.284 AC: 4315 AN: 15182

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1315 AN: 3464

East Asian (EAS) AF: 0.0740 AC: 381 AN: 5152

South Asian (SAS) AF: 0.197 AC: 940 AN: 4770

European-Finnish (FIN) AF: 0.290 AC: 3006 AN: 10374

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.313 AC: 21192 AN: 67804

Other (OTH) AF: 0.381 AC: 801 AN: 2104

Alfa AF: 0.314 Hom.: 15538

Bravo AF: 0.410

Asia WGS AF: 0.140 AC: 488 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.9
DANN	Benign	0.69
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs11241936; hg19: chr5-126978108;