13-104808311-T-C

Variant names:

• chr13-104808311-T-C
• rs323425
• ENST00000807560.1:n.412-2693A>G

Variant summary

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

The ENST00000807560.1(ENSG00000304988):​n.412-2693A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.924 in 152,198 control chromosomes in the GnomAD database, including 65,493 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 0.92 (65493 hom., cov: 32)
• Consequence: ENSG00000304988 ENST00000807560.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.618
• Publications: 0 publications found

Genes affected

ENSG00000304988 (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 (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000807560.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304988	ENST00000807560.1		n.412-2693A>G		intron	N/A
	ENSG00000304988	ENST00000807561.1		n.239-2693A>G		intron	N/A
	ENSG00000304988	ENST00000807562.1		n.321-2693A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.924 AC: 140541 AN: 152080 Hom.: 65461 Cov.: 32

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.968

Gnomad AMR AF: 0.956

Gnomad ASJ AF: 0.953

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.978

Gnomad FIN AF: 0.997

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.973

Gnomad OTH AF: 0.924

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

GnomAD4 genome AF: 0.924 AC: 140632 AN: 152198 Hom.: 65493 Cov.: 32 AF XY: 0.927 AC XY: 68953 AN XY: 74418

African (AFR) AF: 0.795 AC: 32977 AN: 41504

American (AMR) AF: 0.956 AC: 14606 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.953 AC: 3310 AN: 3472

East Asian (EAS) AF: 0.996 AC: 5148 AN: 5170

South Asian (SAS) AF: 0.979 AC: 4731 AN: 4834

European-Finnish (FIN) AF: 0.997 AC: 10585 AN: 10614

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.973 AC: 66181 AN: 68008

Other (OTH) AF: 0.925 AC: 1954 AN: 2112

Alfa AF: 0.957 Hom.: 18508

Bravo AF: 0.915

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.4
DANN	Benign	0.40
PhyloP100		-0.62

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs323425;

hg19: chr13-105460662;