rs10235849

Variant names:

• chr7-35255752-T-A
• rs10235849
• ENST00000692895.2:n.1042T>A

Variant summary

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

The ENST00000692895.2(ENSG00000289335):​n.1042T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 151,750 control chromosomes in the GnomAD database, including 10,017 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 (10017 hom., cov: 32)
• Consequence: ENSG00000289335 ENST00000692895.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.285
• Publications: 2 publications found

Genes affected

ENSG00000289335 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289335	ENST00000692895.2	n.1042T>A		non_coding_transcript_exon_variant	Exon 1 of 1
ENSG00000289335	ENST00000726191.1	n.1042T>A		non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54191 AN: 151632 Hom.: 10006 Cov.: 32

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.357 AC: 54240 AN: 151750 Hom.: 10017 Cov.: 32 AF XY: 0.360 AC XY: 26708 AN XY: 74110

African (AFR) AF: 0.263 AC: 10894 AN: 41422

American (AMR) AF: 0.456 AC: 6949 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.375 AC: 1298 AN: 3462

East Asian (EAS) AF: 0.256 AC: 1320 AN: 5158

South Asian (SAS) AF: 0.383 AC: 1842 AN: 4812

European-Finnish (FIN) AF: 0.415 AC: 4368 AN: 10522

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.390 AC: 26436 AN: 67832

Other (OTH) AF: 0.360 AC: 755 AN: 2100

Alfa AF: 0.375 Hom.: 1346

Bravo AF: 0.356

Asia WGS AF: 0.342 AC: 1189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.6
DANN	Benign	0.78
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs10235849; hg19: chr7-35295363;