chr5-5910544-G-A

Variant names:

• chr5-5910544-G-A
• rs2173946

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 0.338 in 152,044 control chromosomes in the GnomAD database, including 8,936 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 0.34 (8936 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.396 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: 0.339 AC: 51428 AN: 151924 Hom.: 8928 Cov.: 32

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.338 AC: 51459 AN: 152044 Hom.: 8936 Cov.: 32 AF XY: 0.333 AC XY: 24724 AN XY: 74320

African (AFR) AF: 0.317 AC: 13129 AN: 41474

American (AMR) AF: 0.288 AC: 4398 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1055 AN: 3462

East Asian (EAS) AF: 0.411 AC: 2128 AN: 5178

South Asian (SAS) AF: 0.275 AC: 1323 AN: 4814

European-Finnish (FIN) AF: 0.299 AC: 3155 AN: 10558

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.370 AC: 25128 AN: 67972

Other (OTH) AF: 0.302 AC: 635 AN: 2106

Alfa AF: 0.353 Hom.: 29319

Bravo AF: 0.339

Asia WGS AF: 0.335 AC: 1167 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.047
DANN	Benign	0.66
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs2173946; hg19: chr5-5910657;