rs13227425

Positions:

• chr7-13514383-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000639998.1(ENSG00000229618):​n.723-122263C>T 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 0.198 in 152,058 control chromosomes in the GnomAD database, including 3,984 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 0.20 (3984 hom., cov: 32)
• Consequence: ENST00000639998.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.184

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986770	XR_001745097.2	n.148-187933C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000639998.1	n.723-122263C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30061 AN: 151940 Hom.: 3982 Cov.: 32

Gnomad AFR AF: 0.0508

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.0837

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.198 AC: 30053 AN: 152058 Hom.: 3984 Cov.: 32 AF XY: 0.194 AC XY: 14433 AN XY: 74312

Gnomad4 AFR AF: 0.0507

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.252

Gnomad4 EAS AF: 0.00251

Gnomad4 SAS AF: 0.0838

Gnomad4 FIN AF: 0.298

Gnomad4 NFE AF: 0.290

Gnomad4 OTH AF: 0.217

Alfa AF: 0.235 Hom.: 600

Bravo AF: 0.186

Asia WGS AF: 0.0490 AC: 171 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	1.3
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: rs13227425; hg19: chr7-13554008;