5-170102085-C-T

Variant names:

• chr5-170102085-C-T
• rs7704953

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 0.321 in 151,868 control chromosomes in the GnomAD database, including 8,457 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 0.32 (8457 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.227
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.374 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: 0.321 AC: 48681 AN: 151750 Hom.: 8441 Cov.: 31

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.321 AC: 48730 AN: 151868 Hom.: 8457 Cov.: 31 AF XY: 0.321 AC XY: 23828 AN XY: 74208

African (AFR) AF: 0.202 AC: 8357 AN: 41402

American (AMR) AF: 0.349 AC: 5316 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.383 AC: 1329 AN: 3466

East Asian (EAS) AF: 0.179 AC: 923 AN: 5154

South Asian (SAS) AF: 0.341 AC: 1643 AN: 4812

European-Finnish (FIN) AF: 0.426 AC: 4486 AN: 10524

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.378 AC: 25675 AN: 67942

Other (OTH) AF: 0.339 AC: 717 AN: 2114

Alfa AF: 0.358 Hom.: 35326

Bravo AF: 0.312

Asia WGS AF: 0.296 AC: 1030 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.9
DANN	Benign	0.50
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs7704953; hg19: chr5-169529089;