rs17378679

Variant names:

• chr5-72439477-G-C
• rs17378679

Your query was ambiguous. Multiple possible variants found:

• chr5-72439477-G-C
• chr5-72439477-G-T

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 0.0864 in 152,236 control chromosomes in the GnomAD database, including 767 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 0.086 (767 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.529
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.125 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: 0.0864 AC: 13143 AN: 152118 Hom.: 766 Cov.: 32

Gnomad AFR AF: 0.0229

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.0788

Gnomad ASJ AF: 0.0481

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0548

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.0884

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

GnomAD4 genome AF: 0.0864 AC: 13147 AN: 152236 Hom.: 767 Cov.: 32 AF XY: 0.0869 AC XY: 6469 AN XY: 74422

African (AFR) AF: 0.0230 AC: 954 AN: 41544

American (AMR) AF: 0.0787 AC: 1204 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0481 AC: 167 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5184

South Asian (SAS) AF: 0.0551 AC: 266 AN: 4828

European-Finnish (FIN) AF: 0.149 AC: 1583 AN: 10594

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8676 AN: 67996

Other (OTH) AF: 0.0870 AC: 184 AN: 2114

Alfa AF: 0.0640 Hom.: 74

Bravo AF: 0.0772

Asia WGS AF: 0.0290 AC: 102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.3
DANN	Benign	0.70
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs17378679; hg19: chr5-71735304; COSMIC: COSV59214503;