chr5-1764417-C-T

Variant names:

• chr5-1764417-C-T
• rs1107060

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 0.0589 in 152,210 control chromosomes in the GnomAD database, including 493 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 0.059 (493 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.26
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.15 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: 0.0589 AC: 8952 AN: 152092 Hom.: 494 Cov.: 33

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.00440

Gnomad AMR AF: 0.0286

Gnomad ASJ AF: 0.0418

Gnomad EAS AF: 0.00965

Gnomad SAS AF: 0.0309

Gnomad FIN AF: 0.0150

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0226

Gnomad OTH AF: 0.0479

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

GnomAD4 genome AF: 0.0589 AC: 8961 AN: 152210 Hom.: 493 Cov.: 33 AF XY: 0.0582 AC XY: 4331 AN XY: 74432

African (AFR) AF: 0.153 AC: 6366 AN: 41504

American (AMR) AF: 0.0284 AC: 434 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0418 AC: 145 AN: 3472

East Asian (EAS) AF: 0.00967 AC: 50 AN: 5172

South Asian (SAS) AF: 0.0309 AC: 149 AN: 4820

European-Finnish (FIN) AF: 0.0150 AC: 159 AN: 10620

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

European-Non Finnish (NFE) AF: 0.0226 AC: 1537 AN: 68018

Other (OTH) AF: 0.0474 AC: 100 AN: 2108

Alfa AF: 0.0326 Hom.: 472

Bravo AF: 0.0647

Asia WGS AF: 0.0320 AC: 110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.28
DANN	Benign	0.69
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs1107060; hg19: chr5-1764532;