rs2225481

Positions:

• chr13-89145649-A-G
• chr13-89145649-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000661729.1(ENSG00000288552):​n.265-3518T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.672 in 151,816 control chromosomes in the GnomAD database, including 35,520 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 (35520 hom., cov: 32)
• Consequence: ENST00000661729.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.431

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.79 is higher than 0.05.

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
	ENST00000661729.1	n.265-3518T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.672 AC: 101930 AN: 151698 Hom.: 35515 Cov.: 32

Gnomad AFR AF: 0.478

Gnomad AMI AF: 0.855

Gnomad AMR AF: 0.801

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.737

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.752

Gnomad OTH AF: 0.711

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

GnomAD4 genome AF: 0.672 AC: 101962 AN: 151816 Hom.: 35520 Cov.: 32 AF XY: 0.670 AC XY: 49691 AN XY: 74206

Gnomad4 AFR AF: 0.478

Gnomad4 AMR AF: 0.802

Gnomad4 ASJ AF: 0.733

Gnomad4 EAS AF: 0.737

Gnomad4 SAS AF: 0.764

Gnomad4 FIN AF: 0.615

Gnomad4 NFE AF: 0.751

Gnomad4 OTH AF: 0.712

Alfa AF: 0.748 Hom.: 44133

Bravo AF: 0.679

Asia WGS AF: 0.769 AC: 2674 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	6.3
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2225481; hg19: chr13-89797903;