rs1173771

chr5-32814922-A-G

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 0.648 in 152,060 control chromosomes in the GnomAD database, including 32,555 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 0.65 (32555 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.207

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 (AFR) allele frequency at 95% confidence interval = 0.767 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.648 AC: 98392 AN: 151942 Hom.: 32502 Cov.: 32

Gnomad AFR AF: 0.774

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.600

Gnomad ASJ AF: 0.596

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.632

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

GnomAD4 genome AF: 0.648 AC: 98502 AN: 152060 Hom.: 32555 Cov.: 32 AF XY: 0.646 AC XY: 47998 AN XY: 74318

Gnomad4 AFR AF: 0.774

Gnomad4 AMR AF: 0.599

Gnomad4 ASJ AF: 0.596

Gnomad4 EAS AF: 0.650

Gnomad4 SAS AF: 0.600

Gnomad4 FIN AF: 0.592

Gnomad4 NFE AF: 0.597

Gnomad4 OTH AF: 0.635

Alfa AF: 0.608 Hom.: 38263

Bravo AF: 0.653

Asia WGS AF: 0.642 AC: 2232 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	1.7
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1173771; hg19: chr5-32815028;