5-170199971-T-C

Variant names:

• chr5-170199971-T-C
• rs6871985

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.478 in 152,076 control chromosomes in the GnomAD database, including 17,655 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 0.48 (17655 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.36

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.681 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: 0.479 AC: 72727 AN: 151958 Hom.: 17647 Cov.: 32

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.700

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.465

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

GnomAD4 genome AF: 0.478 AC: 72765 AN: 152076 Hom.: 17655 Cov.: 32 AF XY: 0.478 AC XY: 35556 AN XY: 74354

Gnomad4 AFR AF: 0.468

Gnomad4 AMR AF: 0.434

Gnomad4 ASJ AF: 0.428

Gnomad4 EAS AF: 0.700

Gnomad4 SAS AF: 0.454

Gnomad4 FIN AF: 0.482

Gnomad4 NFE AF: 0.480

Gnomad4 OTH AF: 0.469

Alfa AF: 0.330 Hom.: 837

Bravo AF: 0.474

Asia WGS AF: 0.558 AC: 1939 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	15
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6871985; hg19: chr5-169626975;