rs10235849

Positions:

• chr7-35255752-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000692895.1(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: ENST00000692895.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.285

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000692895.1	n.1042T>A		non_coding_transcript_exon_variant	1/1

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

Gnomad4 AFR AF: 0.263

Gnomad4 AMR AF: 0.456

Gnomad4 ASJ AF: 0.375

Gnomad4 EAS AF: 0.256

Gnomad4 SAS AF: 0.383

Gnomad4 FIN AF: 0.415

Gnomad4 NFE AF: 0.390

Gnomad4 OTH AF: 0.360

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10235849; hg19: chr7-35295363;