5-2191323-T-C

Position:

• chr5-2191323-T-C

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 0.642 in 152,044 control chromosomes in the GnomAD database, including 31,545 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 0.64 (31545 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.880

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.642 AC: 97490 AN: 151926 Hom.: 31510 Cov.: 33

Gnomad AFR AF: 0.667

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.700

Gnomad ASJ AF: 0.647

Gnomad EAS AF: 0.611

Gnomad SAS AF: 0.401

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.645

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

GnomAD4 genome AF: 0.642 AC: 97571 AN: 152044 Hom.: 31545 Cov.: 33 AF XY: 0.638 AC XY: 47372 AN XY: 74302

Gnomad4 AFR AF: 0.667

Gnomad4 AMR AF: 0.700

Gnomad4 ASJ AF: 0.647

Gnomad4 EAS AF: 0.611

Gnomad4 SAS AF: 0.400

Gnomad4 FIN AF: 0.658

Gnomad4 NFE AF: 0.632

Gnomad4 OTH AF: 0.641

Alfa AF: 0.632 Hom.: 64803

Bravo AF: 0.652

Asia WGS AF: 0.516 AC: 1797 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	0.034
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11133935; hg19: chr5-2191437;