chr5-151019649-A-C

Variant names:

• chr5-151019649-A-C
• rs1946234

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 0.151 in 152,122 control chromosomes in the GnomAD database, including 1,831 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 0.15 (1831 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.467
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.206 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: 0.151 AC: 23001 AN: 152002 Hom.: 1827 Cov.: 32

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.0955

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.151 AC: 23026 AN: 152122 Hom.: 1831 Cov.: 32 AF XY: 0.149 AC XY: 11052 AN XY: 74390

African (AFR) AF: 0.210 AC: 8703 AN: 41464

American (AMR) AF: 0.0953 AC: 1457 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 449 AN: 3470

East Asian (EAS) AF: 0.171 AC: 887 AN: 5176

South Asian (SAS) AF: 0.151 AC: 727 AN: 4820

European-Finnish (FIN) AF: 0.110 AC: 1171 AN: 10602

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.133 AC: 9059 AN: 67990

Other (OTH) AF: 0.138 AC: 292 AN: 2112

Alfa AF: 0.134 Hom.: 2426

Bravo AF: 0.151

Asia WGS AF: 0.152 AC: 530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.23
DANN	Benign	0.41
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs1946234; hg19: chr5-150399210;