rs2740980

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000651802.1(ENSG00000291034):​n.451-70793C>T variant causes a intron, non coding transcript 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: ENST00000651802.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High Hemizygotes in GnomAd4 at 847 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000651802.1	n.451-70793C>T		intron_variant, non_coding_transcript_variant
	ENST00000651835.1	n.320-54170C>T		intron_variant, non_coding_transcript_variant

Frequencies

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

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

Gnomad4 AFR AF: 0.00511

Gnomad4 AMR AF: 0.0508

Gnomad4 ASJ AF: 0.0827

Gnomad4 EAS AF: 0.000797

Gnomad4 SAS AF: 0.0298

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0338

Gnomad4 OTH AF: 0.0277

Alfa AF: 0.0340 Hom.: 659

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2740980; hg19: chrY-14432928;