7-136276051-C-T

Variant names:

• chr7-136276051-C-T
• rs7811360
• ENST00000435996.1:n.243-52931C>T

Variant summary

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

The ENST00000435996.1(ENSG00000232053):​n.243-52931C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0807 in 151,886 control chromosomes in the GnomAD database, including 547 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 0.081 (547 hom., cov: 31)
• Consequence: ENSG00000232053 ENST00000435996.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.976
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0852 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_187956.1		n.275-52931C>T		intron	N/A
	LOC105375523	NR_187957.1		n.614+33680C>T		intron	N/A
	LOC105375523	NR_187960.1		n.614+33680C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000232053	ENST00000435996.1	TSL:3	n.243-52931C>T		intron	N/A
	ENSG00000232053	ENST00000445293.6	TSL:5	n.614+33680C>T		intron	N/A
	ENSG00000232053	ENST00000657456.1		n.508+33680C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0807 AC: 12246 AN: 151768 Hom.: 541 Cov.: 31

Gnomad AFR AF: 0.0762

Gnomad AMI AF: 0.0231

Gnomad AMR AF: 0.0529

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.000964

Gnomad SAS AF: 0.0657

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0871

Gnomad OTH AF: 0.0763

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

GnomAD4 genome AF: 0.0807 AC: 12263 AN: 151886 Hom.: 547 Cov.: 31 AF XY: 0.0819 AC XY: 6080 AN XY: 74212

African (AFR) AF: 0.0766 AC: 3171 AN: 41404

American (AMR) AF: 0.0528 AC: 804 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 465 AN: 3472

East Asian (EAS) AF: 0.000966 AC: 5 AN: 5176

South Asian (SAS) AF: 0.0658 AC: 317 AN: 4820

European-Finnish (FIN) AF: 0.131 AC: 1380 AN: 10522

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0870 AC: 5913 AN: 67958

Other (OTH) AF: 0.0755 AC: 159 AN: 2106

Alfa AF: 0.0819 Hom.: 904

Bravo AF: 0.0744

Asia WGS AF: 0.0280 AC: 98 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.095
DANN	Benign	0.64
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs7811360; hg19: chr7-135960799;