rs1365353

Variant names:

• chr7-136258516-G-A
• rs1365353
• ENST00000435996.1:n.243-70466G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000435996.1(ENSG00000232053):​n.243-70466G>A variant causes a intron 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: ENSG00000232053 ENST00000435996.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.185
• Publications: 2 publications found

Genes affected

ENSG00000232053 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105375523	NR_187956.1	n.275-70466G>A		intron_variant	Intron 2 of 4
LOC105375523	NR_187957.1	n.614+16145G>A		intron_variant	Intron 4 of 5
LOC105375523	NR_187960.1	n.614+16145G>A		intron_variant	Intron 4 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000232053	ENST00000435996.1	n.243-70466G>A		intron_variant	Intron 2 of 3	3
ENSG00000232053	ENST00000445293.6	n.614+16145G>A		intron_variant	Intron 4 of 6	5
ENSG00000232053	ENST00000657456.1	n.508+16145G>A		intron_variant	Intron 3 of 4

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

African (AFR) AF: 0.317 AC: 13160 AN: 41456

American (AMR) AF: 0.404 AC: 6174 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.440 AC: 1523 AN: 3464

East Asian (EAS) AF: 0.723 AC: 3734 AN: 5162

South Asian (SAS) AF: 0.452 AC: 2179 AN: 4816

European-Finnish (FIN) AF: 0.393 AC: 4142 AN: 10536

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.429 AC: 29146 AN: 67936

Other (OTH) AF: 0.405 AC: 852 AN: 2106

Alfa AF: 0.417 Hom.: 7148

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
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs1365353; hg19: chr7-135943264;