chr13-42724916-G-A

Variant names:

• chr13-42724916-G-A
• rs7993057
• ENST00000799325.1:n.356-4215C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000799325.1(ENSG00000304062):​n.356-4215C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.932 in 152,272 control chromosomes in the GnomAD database, including 66,568 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 0.93 (66568 hom., cov: 33)
• Consequence: ENSG00000304062 ENST00000799325.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.837
• Publications: 1 publications found

Genes affected

ENSG00000304062 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000799325.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304062	ENST00000799325.1		n.356-4215C>T		intron	N/A
	ENSG00000304062	ENST00000799326.1		n.762-4215C>T		intron	N/A
	ENSG00000304062	ENST00000799327.1		n.359-4215C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.933 AC: 141889 AN: 152154 Hom.: 66536 Cov.: 33

Gnomad AFR AF: 0.815

Gnomad AMI AF: 0.979

Gnomad AMR AF: 0.964

Gnomad ASJ AF: 0.989

Gnomad EAS AF: 0.980

Gnomad SAS AF: 0.983

Gnomad FIN AF: 0.972

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.980

Gnomad OTH AF: 0.946

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

GnomAD4 genome AF: 0.932 AC: 141978 AN: 152272 Hom.: 66568 Cov.: 33 AF XY: 0.934 AC XY: 69513 AN XY: 74450

African (AFR) AF: 0.815 AC: 33838 AN: 41532

American (AMR) AF: 0.964 AC: 14745 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.989 AC: 3433 AN: 3470

East Asian (EAS) AF: 0.980 AC: 5084 AN: 5188

South Asian (SAS) AF: 0.983 AC: 4749 AN: 4830

European-Finnish (FIN) AF: 0.972 AC: 10320 AN: 10618

Middle Eastern (MID) AF: 0.939 AC: 276 AN: 294

European-Non Finnish (NFE) AF: 0.980 AC: 66645 AN: 68030

Other (OTH) AF: 0.945 AC: 1995 AN: 2110

Alfa AF: 0.957 Hom.: 33488

Bravo AF: 0.928

Asia WGS AF: 0.954 AC: 3318 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.20
DANN	Benign	0.56
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs7993057; hg19: chr13-43299052;