rs71645904

Variant names:

• chr5-132672464-G-A
• rs71645904

Your query was ambiguous. Multiple possible variants found:

• chr5-132672464-G-A
• chr5-132672464-G-C

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 0.0221 in 147,714 control chromosomes in the GnomAD database, including 151 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 0.022 (151 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0581 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: 0.0220 AC: 3248 AN: 147594 Hom.: 148 Cov.: 27

Gnomad AFR AF: 0.0289

Gnomad AMI AF: 0.00111

Gnomad AMR AF: 0.0613

Gnomad ASJ AF: 0.0182

Gnomad EAS AF: 0.0550

Gnomad SAS AF: 0.0463

Gnomad FIN AF: 0.00109

Gnomad MID AF: 0.0276

Gnomad NFE AF: 0.00845

Gnomad OTH AF: 0.0258

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

GnomAD4 genome AF: 0.0221 AC: 3269 AN: 147714 Hom.: 151 Cov.: 27 AF XY: 0.0236 AC XY: 1697 AN XY: 72030

African (AFR) AF: 0.0293 AC: 1189 AN: 40606

American (AMR) AF: 0.0615 AC: 906 AN: 14740

Ashkenazi Jewish (ASJ) AF: 0.0182 AC: 62 AN: 3410

East Asian (EAS) AF: 0.0552 AC: 274 AN: 4966

South Asian (SAS) AF: 0.0463 AC: 207 AN: 4470

European-Finnish (FIN) AF: 0.00109 AC: 11 AN: 10070

Middle Eastern (MID) AF: 0.0255 AC: 7 AN: 274

European-Non Finnish (NFE) AF: 0.00845 AC: 560 AN: 66284

Other (OTH) AF: 0.0261 AC: 52 AN: 1994

Alfa AF: 0.000378 Hom.: 0

Bravo AF: 0.0274

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.48
DANN	Benign	0.43
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs71645904; hg19: chr5-132008156;