rs1365360

Positions:

• chr7-136227937-T-A

Variant summary

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

The ENST00000668062.1(ENSG00000232053):​n.115-14213T>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 0.129 in 152,188 control chromosomes in the GnomAD database, including 1,389 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 0.13 (1389 hom., cov: 33)
• Consequence: ENST00000668062.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.295

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375523	XR_007060545.1	n.527-14213T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000668062.1	n.115-14213T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19667 AN: 152070 Hom.: 1391 Cov.: 33

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.0845

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.129 AC: 19674 AN: 152188 Hom.: 1389 Cov.: 33 AF XY: 0.129 AC XY: 9611 AN XY: 74406

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.0845

Gnomad4 ASJ AF: 0.211

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.190

Gnomad4 FIN AF: 0.130

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.127

Alfa AF: 0.133 Hom.: 176

Bravo AF: 0.123

Asia WGS AF: 0.0770 AC: 269 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1365360; hg19: chr7-135912685;