rs2740980

Variant names:

• chrY-12312201-G-A
• rs2740980
• ENST00000651802.1:n.451-70793C>T

Your query was ambiguous. Multiple possible variants found:

• chrY-12312201-G-A
• chrY-12312201-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000651802.1(ENSG00000291034):​n.451-70793C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.025 (0 hom., 847 hem., cov: 0)
• Consequence: ENSG00000291034 ENST00000651802.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640
• Publications: 4 publications found

Genes affected

ENSG00000291034 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BS1: Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.0253 (847/33457) while in subpopulation AMR AF = 0.0508 (185/3640). AF 95% confidence interval is 0.0448. There are 0 homozygotes in GnomAd4. There are 847 alleles in the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.
• BS2: High Hemizygotes in GnomAd4 at 847 gene

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
ENSG00000291034	ENST00000651802.1	n.451-70793C>T		intron_variant	Intron 4 of 9
ENSG00000291034	ENST00000651835.1	n.320-54170C>T		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes AF: 0.0253 AC: 844 AN: 33392 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00514

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.0509

Gnomad ASJ AF: 0.0827

Gnomad EAS AF: 0.000797

Gnomad SAS AF: 0.0292

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.183

Gnomad NFE AF: 0.0337

Gnomad OTH AF: 0.0278

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

GnomAD4 genome AF: 0.0253 AC: 847 AN: 33457 Hom.: 0 Cov.: 0 AF XY: 0.0253 AC XY: 847 AN XY: 33457

African (AFR) AF: 0.00511 AC: 44 AN: 8618

American (AMR) AF: 0.0508 AC: 185 AN: 3640

Ashkenazi Jewish (ASJ) AF: 0.0827 AC: 64 AN: 774

East Asian (EAS) AF: 0.000797 AC: 1 AN: 1254

South Asian (SAS) AF: 0.0298 AC: 43 AN: 1443

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 3436

Middle Eastern (MID) AF: 0.183 AC: 13 AN: 71

European-Non Finnish (NFE) AF: 0.0338 AC: 458 AN: 13542

Other (OTH) AF: 0.0277 AC: 13 AN: 470

Alfa AF: 0.0436 Hom.: 873

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.2
PhyloP100		0.064

Splicing

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

Other links and lift over

dbSNP: rs2740980; hg19: chrY-14432928;