chr5-149657413-T-C

Variant names:

• chr5-149657413-T-C
• rs17710780

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.1 in 152,254 control chromosomes in the GnomAD database, including 971 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 0.10 (971 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.285

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.16 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: 0.100 AC: 15228 AN: 152136 Hom.: 971 Cov.: 32

Gnomad AFR AF: 0.0234

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.0795

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.100 AC: 15221 AN: 152254 Hom.: 971 Cov.: 32 AF XY: 0.102 AC XY: 7599 AN XY: 74438

Gnomad4 AFR AF: 0.0233

Gnomad4 AMR AF: 0.146

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.0787

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.122

Alfa AF: 0.112 Hom.: 516

Bravo AF: 0.100

Asia WGS AF: 0.111 AC: 388 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.1
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17710780; hg19: chr5-149036976;