chr7-136227937-T-A

Variant names:

• chr7-136227937-T-A
• rs1365360
• ENST00000435996.1:n.242+50524T>A

Variant summary

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

The ENST00000435996.1(ENSG00000232053):​n.242+50524T>A variant causes a intron 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: ENSG00000232053 ENST00000435996.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.295
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000435996.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105375523	NR_187952.1		n.113-14213T>A		intron	N/A
	LOC105375523	NR_187953.1		n.315-14213T>A		intron	N/A
	LOC105375523	NR_187954.1		n.421-14213T>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000232053	ENST00000435996.1	TSL:3	n.242+50524T>A		intron	N/A
	ENSG00000232053	ENST00000445293.6	TSL:5	n.393-14213T>A		intron	N/A
	ENSG00000232053	ENST00000657456.1		n.287-14213T>A		intron	N/A

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

African (AFR) AF: 0.128 AC: 5323 AN: 41530

American (AMR) AF: 0.0845 AC: 1291 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 730 AN: 3464

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5182

South Asian (SAS) AF: 0.190 AC: 915 AN: 4826

European-Finnish (FIN) AF: 0.130 AC: 1371 AN: 10580

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.142 AC: 9647 AN: 68008

Other (OTH) AF: 0.127 AC: 268 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.68
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs1365360; hg19: chr7-135912685;