rs71627250

Variant names:

• chr5-63088872-C-T
• rs71627250

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 0.0648 in 152,188 control chromosomes in the GnomAD database, including 336 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 0.065 (336 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.65
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.165 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: 0.0649 AC: 9862 AN: 152070 Hom.: 335 Cov.: 32

Gnomad AFR AF: 0.0847

Gnomad AMI AF: 0.0758

Gnomad AMR AF: 0.0652

Gnomad ASJ AF: 0.0346

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.0362

Gnomad FIN AF: 0.0454

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0506

Gnomad OTH AF: 0.0722

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

GnomAD4 genome AF: 0.0648 AC: 9859 AN: 152188 Hom.: 336 Cov.: 32 AF XY: 0.0641 AC XY: 4771 AN XY: 74410

African (AFR) AF: 0.0846 AC: 3510 AN: 41512

American (AMR) AF: 0.0652 AC: 997 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0346 AC: 120 AN: 3472

East Asian (EAS) AF: 0.175 AC: 903 AN: 5172

South Asian (SAS) AF: 0.0362 AC: 175 AN: 4834

European-Finnish (FIN) AF: 0.0454 AC: 480 AN: 10582

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0506 AC: 3443 AN: 68008

Other (OTH) AF: 0.0710 AC: 150 AN: 2112

Alfa AF: 0.0574 Hom.: 57

Bravo AF: 0.0717

Asia WGS AF: 0.0850 AC: 295 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	6.7
DANN	Benign	0.45
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs71627250; hg19: chr5-62384699;