chr7-13597906-T-A

Variant names:

• chr7-13597906-T-A
• rs1568885
• ENST00000411542.1:n.352-38740T>A

Variant summary

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

The ENST00000411542.1(ENSG00000229618):​n.352-38740T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 151,826 control chromosomes in the GnomAD database, including 1,226 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 0.12 (1226 hom., cov: 32)
• Consequence: ENSG00000229618 ENST00000411542.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17
• Publications: 15 publications found

Genes affected

ENSG00000229618 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986770	XR_001745097.2	n.148-104410T>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000229618	ENST00000411542.1	n.352-38740T>A		intron_variant	Intron 3 of 4	4
ENSG00000229618	ENST00000638964.1	n.724-38740T>A		intron_variant	Intron 3 of 5	5
ENSG00000229618	ENST00000639998.1	n.723-38740T>A		intron_variant	Intron 5 of 7	5

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17929 AN: 151708 Hom.: 1221 Cov.: 32

Gnomad AFR AF: 0.0744

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.0116

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.118 AC: 17946 AN: 151826 Hom.: 1226 Cov.: 32 AF XY: 0.116 AC XY: 8589 AN XY: 74218

African (AFR) AF: 0.0743 AC: 3083 AN: 41488

American (AMR) AF: 0.104 AC: 1588 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 583 AN: 3462

East Asian (EAS) AF: 0.0116 AC: 60 AN: 5166

South Asian (SAS) AF: 0.144 AC: 696 AN: 4828

European-Finnish (FIN) AF: 0.103 AC: 1095 AN: 10588

Middle Eastern (MID) AF: 0.175 AC: 51 AN: 292

European-Non Finnish (NFE) AF: 0.153 AC: 10342 AN: 67756

Other (OTH) AF: 0.131 AC: 275 AN: 2106

Alfa AF: 0.134 Hom.: 177

Bravo AF: 0.116

Asia WGS AF: 0.0880 AC: 308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	16
DANN	Benign	0.55
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs1568885; hg19: chr7-13637531;