rs2165985

Positions:

• chr13-53402639-A-C
• chr13-53402639-A-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000615176.1(ENSG00000273919):​n.977-7361A>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 0.435 in 151,998 control chromosomes in the GnomAD database, including 14,749 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 0.44 (14749 hom., cov: 33)
• Consequence: ENST00000615176.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.172

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000615176.1	n.977-7361A>C		intron_variant, non_coding_transcript_variant		2
	ENST00000657016.1	n.629+98517A>C		intron_variant, non_coding_transcript_variant
	ENST00000688155.1	n.46-20141A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66083 AN: 151878 Hom.: 14741 Cov.: 33

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.448

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.435 AC: 66126 AN: 151998 Hom.: 14749 Cov.: 33 AF XY: 0.438 AC XY: 32571 AN XY: 74280

Gnomad4 AFR AF: 0.367

Gnomad4 AMR AF: 0.524

Gnomad4 ASJ AF: 0.459

Gnomad4 EAS AF: 0.450

Gnomad4 SAS AF: 0.474

Gnomad4 FIN AF: 0.445

Gnomad4 NFE AF: 0.448

Gnomad4 OTH AF: 0.457

Alfa AF: 0.379 Hom.: 1953

Bravo AF: 0.439

Asia WGS AF: 0.456 AC: 1581 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	17
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2165985; hg19: chr13-53976774;