chr5-71722730-A-T

Variant names:

• chr5-71722730-A-T
• rs16871471

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 0.204 in 152,210 control chromosomes in the GnomAD database, including 3,369 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 0.20 (3369 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.261 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: 0.204 AC: 30979 AN: 152092 Hom.: 3363 Cov.: 31

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.204 AC: 31006 AN: 152210 Hom.: 3369 Cov.: 31 AF XY: 0.204 AC XY: 15176 AN XY: 74386

African (AFR) AF: 0.237 AC: 9856 AN: 41526

American (AMR) AF: 0.268 AC: 4097 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 423 AN: 3470

East Asian (EAS) AF: 0.103 AC: 536 AN: 5184

South Asian (SAS) AF: 0.239 AC: 1153 AN: 4828

European-Finnish (FIN) AF: 0.209 AC: 2209 AN: 10578

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.179 AC: 12203 AN: 68016

Other (OTH) AF: 0.167 AC: 354 AN: 2116

Alfa AF: 0.190 Hom.: 328

Bravo AF: 0.207

Asia WGS AF: 0.183 AC: 634 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	6.5
DANN	Benign	0.87
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs16871471; hg19: chr5-71018557;