chr5-25840341-T-C

Variant names:

• chr5-25840341-T-C
• rs10065041

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 0.673 in 152,078 control chromosomes in the GnomAD database, including 35,018 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 0.67 (35018 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.07
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.789 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: 0.673 AC: 102277 AN: 151958 Hom.: 34983 Cov.: 32

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.696

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.743

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.658

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

GnomAD4 genome AF: 0.673 AC: 102369 AN: 152078 Hom.: 35018 Cov.: 32 AF XY: 0.671 AC XY: 49887 AN XY: 74346

African (AFR) AF: 0.796 AC: 33029 AN: 41502

American (AMR) AF: 0.696 AC: 10644 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.534 AC: 1853 AN: 3472

East Asian (EAS) AF: 0.743 AC: 3829 AN: 5156

South Asian (SAS) AF: 0.601 AC: 2895 AN: 4814

European-Finnish (FIN) AF: 0.614 AC: 6488 AN: 10568

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.611 AC: 41496 AN: 67962

Other (OTH) AF: 0.656 AC: 1389 AN: 2116

Alfa AF: 0.632 Hom.: 17843

Bravo AF: 0.686

Asia WGS AF: 0.682 AC: 2374 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.55
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs10065041; hg19: chr5-25840450;