ENST00000435996.1:n.243-55386A>G

Variant names:

• chr7-136273596-A-G
• rs1035786
• ENST00000435996.1:n.243-55386A>G

Variant summary

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

The ENST00000435996.1(ENSG00000232053):​n.243-55386A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.969 in 152,186 control chromosomes in the GnomAD database, including 71,683 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 0.97 (71683 hom., cov: 30)
• Consequence: ENSG00000232053 ENST00000435996.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.291
• Publications: 1 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375523	NR_187956.1	n.275-55386A>G		intron_variant	Intron 2 of 4
LOC105375523	NR_187957.1	n.614+31225A>G		intron_variant	Intron 4 of 5
LOC105375523	NR_187960.1	n.614+31225A>G		intron_variant	Intron 4 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000232053	ENST00000435996.1	n.243-55386A>G		intron_variant	Intron 2 of 3	3
ENSG00000232053	ENST00000445293.6	n.614+31225A>G		intron_variant	Intron 4 of 6	5
ENSG00000232053	ENST00000657456.1	n.508+31225A>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.969 AC: 147411 AN: 152068 Hom.: 71630 Cov.: 30

Gnomad AFR AF: 0.894

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.991

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.993

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.997

Gnomad NFE AF: 1.00

Gnomad OTH AF: 0.976

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

GnomAD4 genome AF: 0.969 AC: 147523 AN: 152186 Hom.: 71683 Cov.: 30 AF XY: 0.971 AC XY: 72224 AN XY: 74416

African (AFR) AF: 0.894 AC: 37082 AN: 41496

American (AMR) AF: 0.991 AC: 15141 AN: 15286

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 3470 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5162 AN: 5162

South Asian (SAS) AF: 0.994 AC: 4794 AN: 4824

European-Finnish (FIN) AF: 1.00 AC: 10620 AN: 10620

Middle Eastern (MID) AF: 0.997 AC: 293 AN: 294

European-Non Finnish (NFE) AF: 1.00 AC: 67989 AN: 68012

Other (OTH) AF: 0.976 AC: 2062 AN: 2112

Alfa AF: 0.982 Hom.: 4372

Bravo AF: 0.965

Asia WGS AF: 0.991 AC: 3446 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.70
DANN	Benign	0.72
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs1035786; hg19: chr7-135958344;