rs1365353

Positions:

• chr7-136258516-G-A
• chr7-136258516-G-C
• chr7-136258516-G-T

Variant summary

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

The ENST00000668062.1(ENSG00000232053):​n.336+16145G>A 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 0.403 in 151,948 control chromosomes in the GnomAD database, including 12,866 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 0.40 (12866 hom., cov: 32)
• Consequence: ENST00000668062.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.185

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375523	XR_007060545.1	n.748+16145G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000668062.1	n.336+16145G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61277 AN: 151830 Hom.: 12856 Cov.: 32

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.723

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.403 AC: 61301 AN: 151948 Hom.: 12866 Cov.: 32 AF XY: 0.406 AC XY: 30108 AN XY: 74248

Gnomad4 AFR AF: 0.317

Gnomad4 AMR AF: 0.404

Gnomad4 ASJ AF: 0.440

Gnomad4 EAS AF: 0.723

Gnomad4 SAS AF: 0.452

Gnomad4 FIN AF: 0.393

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.405

Alfa AF: 0.417 Hom.: 6431

Bravo AF: 0.401

Asia WGS AF: 0.563 AC: 1954 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.5
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1365353; hg19: chr7-135943264;