rs1568885

Positions:

• chr7-13597906-T-A

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000229618 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC107986770	XR_001745097.2	n.148-104410T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000229618	ENST00000411542.1	n.352-38740T>A		intron_variant		4
ENSG00000229618	ENST00000638964.1	n.724-38740T>A		intron_variant		5
ENSG00000229618	ENST00000639998.1	n.723-38740T>A		intron_variant		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

Gnomad4 AFR AF: 0.0743

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.168

Gnomad4 EAS AF: 0.0116

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.103

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.131

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1568885; hg19: chr7-13637531;