rs834789

Variant names:

• chr7-136177559-T-C
• rs834789
• ENST00000435996.1:n.242+146T>C

Variant summary

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

The ENST00000435996.1(ENSG00000232053):​n.242+146T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 152,000 control chromosomes in the GnomAD database, including 12,404 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 0.36 (12403 hom., cov: 32)
  • Exomes 𝑓: 0.36 (1 hom.)
• Consequence: ENSG00000232053 ENST00000435996.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.393
• 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 = 0.634 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.113-64591T>C		intron	N/A
	LOC105375523	NR_187953.1		n.314+146T>C		intron	N/A
	LOC105375523	NR_187954.1		n.420+146T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000232053	ENST00000435996.1	TSL:3	n.242+146T>C		intron	N/A
	ENSG00000232053	ENST00000445293.6	TSL:5	n.392+146T>C		intron	N/A
	ENSG00000232053	ENST00000657456.1		n.286+146T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.362 AC: 55027 AN: 151868 Hom.: 12379 Cov.: 32

Gnomad AFR AF: 0.641

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.0251

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.326

GnomAD4 exome AF: 0.357 AC: 5 AN: 14 Hom.: 1 AF XY: 0.333 AC XY: 4 AN XY: 12

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.357 AC: 5 AN: 14

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.362 AC: 55093 AN: 151986 Hom.: 12403 Cov.: 32 AF XY: 0.356 AC XY: 26485 AN XY: 74312

African (AFR) AF: 0.640 AC: 26536 AN: 41432

American (AMR) AF: 0.224 AC: 3414 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 887 AN: 3472

East Asian (EAS) AF: 0.0252 AC: 130 AN: 5168

South Asian (SAS) AF: 0.281 AC: 1354 AN: 4810

European-Finnish (FIN) AF: 0.231 AC: 2440 AN: 10584

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.283 AC: 19239 AN: 67946

Other (OTH) AF: 0.323 AC: 681 AN: 2106

Alfa AF: 0.324 Hom.: 1540

Bravo AF: 0.372

Asia WGS AF: 0.184 AC: 642 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	0.12
DANN	Benign	0.75
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs834789; hg19: chr7-135862307;