7-136140776-A-G

Variant names:

• chr7-136140776-A-G
• rs10488401
• ENST00000435996.1:n.81-36476A>G

Variant summary

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

The ENST00000435996.1(ENSG00000232053):​n.81-36476A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.622 in 152,092 control chromosomes in the GnomAD database, including 32,253 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 0.62 (32253 hom., cov: 33)
• Consequence: ENSG00000232053 ENST00000435996.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 4 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 (AFR) allele frequency at 95% confidence interval = 0.877 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105375523	NR_187952.1		n.113-101374A>G		intron	N/A
	LOC105375523	NR_187953.1		n.153-36476A>G		intron	N/A
	LOC105375523	NR_187954.1		n.259-36476A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000232053	ENST00000435996.1	TSL:3	n.81-36476A>G		intron	N/A
	ENSG00000232053	ENST00000445293.6	TSL:5	n.230+23588A>G		intron	N/A
	ENSG00000232053	ENST00000657456.1		n.125-36476A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94497 AN: 151974 Hom.: 32199 Cov.: 33

Gnomad AFR AF: 0.884

Gnomad AMI AF: 0.637

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.0993

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.593

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

GnomAD4 genome AF: 0.622 AC: 94591 AN: 152092 Hom.: 32253 Cov.: 33 AF XY: 0.609 AC XY: 45266 AN XY: 74356

African (AFR) AF: 0.885 AC: 36723 AN: 41516

American (AMR) AF: 0.438 AC: 6696 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.642 AC: 2227 AN: 3468

East Asian (EAS) AF: 0.0992 AC: 514 AN: 5182

South Asian (SAS) AF: 0.484 AC: 2329 AN: 4816

European-Finnish (FIN) AF: 0.496 AC: 5235 AN: 10564

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.572 AC: 38877 AN: 67940

Other (OTH) AF: 0.586 AC: 1237 AN: 2110

Alfa AF: 0.591 Hom.: 5568

Bravo AF: 0.625

Asia WGS AF: 0.338 AC: 1176 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.15
DANN	Benign	0.45
PhyloP100		-1.2
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

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

Other links and lift over

dbSNP: rs10488401; hg19: chr7-135825524;