5-71722230-T-C

Variant names:

• chr5-71722230-T-C
• rs17358300

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 0.453 in 151,332 control chromosomes in the GnomAD database, including 17,649 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 0.45 (17649 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.705 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: 0.453 AC: 68537 AN: 151214 Hom.: 17613 Cov.: 30

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.453 AC: 68625 AN: 151332 Hom.: 17649 Cov.: 30 AF XY: 0.449 AC XY: 33182 AN XY: 73950

African (AFR) AF: 0.712 AC: 29325 AN: 41200

American (AMR) AF: 0.435 AC: 6599 AN: 15176

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1156 AN: 3464

East Asian (EAS) AF: 0.396 AC: 2038 AN: 5148

South Asian (SAS) AF: 0.498 AC: 2376 AN: 4768

European-Finnish (FIN) AF: 0.301 AC: 3127 AN: 10380

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22612 AN: 67894

Other (OTH) AF: 0.412 AC: 865 AN: 2102

Alfa AF: 0.432 Hom.: 2264

Bravo AF: 0.471

Asia WGS AF: 0.458 AC: 1596 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.38
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs17358300; hg19: chr5-71018057;