chr5-101874544-G-A

Position:

• chr5-101874544-G-A

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 0.827 in 152,078 control chromosomes in the GnomAD database, including 52,238 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 0.83 (52238 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.253

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.948 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: 0.827 AC: 125688 AN: 151960 Hom.: 52199 Cov.: 31

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.853

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.970

Gnomad SAS AF: 0.936

Gnomad FIN AF: 0.845

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.810

Gnomad OTH AF: 0.808

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

GnomAD4 genome AF: 0.827 AC: 125778 AN: 152078 Hom.: 52238 Cov.: 31 AF XY: 0.831 AC XY: 61811 AN XY: 74340

Gnomad4 AFR AF: 0.823

Gnomad4 AMR AF: 0.853

Gnomad4 ASJ AF: 0.690

Gnomad4 EAS AF: 0.970

Gnomad4 SAS AF: 0.936

Gnomad4 FIN AF: 0.845

Gnomad4 NFE AF: 0.810

Gnomad4 OTH AF: 0.810

Alfa AF: 0.799 Hom.: 5361

Bravo AF: 0.827

Asia WGS AF: 0.943 AC: 3275 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.6
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7731840; hg19: chr5-101210248;