chr15-63041420-A-G

Variant names:

• chr15-63041420-A-G
• rs3809565
• ENST00000804116.1:n.122+7145T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000804116.1(TPM1-AS):​n.122+7145T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.696 in 152,206 control chromosomes in the GnomAD database, including 37,029 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 0.70 (37029 hom., cov: 34)
• Consequence: TPM1-AS ENST00000804116.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.13
• Publications: 7 publications found

Genes affected

TPM1-AS (HGNC:53635): (TPM1 antisense RNA)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.745 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
TPM1-AS	ENST00000804116.1	n.122+7145T>C		intron_variant	Intron 1 of 3
TPM1-AS	ENST00000804117.1	n.171+1968T>C		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.696 AC: 105867 AN: 152088 Hom.: 36990 Cov.: 34

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.698

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.698

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

GnomAD4 genome AF: 0.696 AC: 105954 AN: 152206 Hom.: 37029 Cov.: 34 AF XY: 0.692 AC XY: 51480 AN XY: 74394

African (AFR) AF: 0.722 AC: 29986 AN: 41548

American (AMR) AF: 0.757 AC: 11580 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.698 AC: 2425 AN: 3472

East Asian (EAS) AF: 0.544 AC: 2811 AN: 5166

South Asian (SAS) AF: 0.566 AC: 2732 AN: 4824

European-Finnish (FIN) AF: 0.667 AC: 7054 AN: 10580

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.694 AC: 47212 AN: 67998

Other (OTH) AF: 0.694 AC: 1467 AN: 2114

Alfa AF: 0.696 Hom.: 48912

Bravo AF: 0.705

Asia WGS AF: 0.552 AC: 1919 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	17
DANN	Benign	0.70
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs3809565; hg19: chr15-63333619;