chr15-34831869-T-G

Variant names:

• chr15-34831869-T-G
• rs1901417

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 0.0657 in 152,300 control chromosomes in the GnomAD database, including 550 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 0.066 (550 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.139 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: 0.0656 AC: 9990 AN: 152182 Hom.: 548 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0495

Gnomad ASJ AF: 0.0527

Gnomad EAS AF: 0.0534

Gnomad SAS AF: 0.0304

Gnomad FIN AF: 0.0109

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0366

Gnomad OTH AF: 0.0598

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

GnomAD4 genome AF: 0.0657 AC: 10011 AN: 152300 Hom.: 550 Cov.: 32 AF XY: 0.0637 AC XY: 4742 AN XY: 74480

African (AFR) AF: 0.142 AC: 5900 AN: 41546

American (AMR) AF: 0.0494 AC: 756 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0527 AC: 183 AN: 3470

East Asian (EAS) AF: 0.0535 AC: 278 AN: 5192

South Asian (SAS) AF: 0.0296 AC: 143 AN: 4826

European-Finnish (FIN) AF: 0.0109 AC: 116 AN: 10620

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

European-Non Finnish (NFE) AF: 0.0366 AC: 2491 AN: 68028

Other (OTH) AF: 0.0591 AC: 125 AN: 2114

Alfa AF: 0.0182 Hom.: 18

Bravo AF: 0.0703

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.20
DANN	Benign	0.61
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1901417; hg19: chr15-35124070;