rs747942

Variant names:

• chr10-69576710-T-C
• rs747942
• ENST00000839710.1:n.1761T>C

Your query was ambiguous. Multiple possible variants found:

• chr10-69576710-T-C
• chr10-69576710-T-G

Variant summary

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

The ENST00000839710.1(ENSG00000236154):​n.1761T>C 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 0.0719 in 152,120 control chromosomes in the GnomAD database, including 1,248 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 0.072 (1248 hom., cov: 32)
• Consequence: ENSG00000236154 ENST00000839710.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.264
• Publications: 1 publications found

Genes affected

ENSG00000236154 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101929021	XR_428765.3	n.231-273T>C		intron_variant	Intron 2 of 2
LOC101929021	XR_946037.2	n.498-273T>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000236154	ENST00000839710.1	n.1761T>C		non_coding_transcript_exon_variant	Exon 1 of 1
ENSG00000236154	ENST00000428753.2	n.1206-273T>C		intron_variant	Intron 1 of 1	3
ENSG00000236154	ENST00000685746.3	n.766-273T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0717 AC: 10906 AN: 152002 Hom.: 1244 Cov.: 32

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0293

Gnomad ASJ AF: 0.0147

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0530

Gnomad FIN AF: 0.000283

Gnomad MID AF: 0.0510

Gnomad NFE AF: 0.00112

Gnomad OTH AF: 0.0589

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

GnomAD4 genome AF: 0.0719 AC: 10939 AN: 152120 Hom.: 1248 Cov.: 32 AF XY: 0.0714 AC XY: 5308 AN XY: 74376

African (AFR) AF: 0.240 AC: 9963 AN: 41428

American (AMR) AF: 0.0293 AC: 448 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0147 AC: 51 AN: 3468

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5176

South Asian (SAS) AF: 0.0533 AC: 257 AN: 4822

European-Finnish (FIN) AF: 0.000283 AC: 3 AN: 10602

Middle Eastern (MID) AF: 0.0548 AC: 16 AN: 292

European-Non Finnish (NFE) AF: 0.00112 AC: 76 AN: 68012

Other (OTH) AF: 0.0583 AC: 123 AN: 2110

Alfa AF: 0.0211 Hom.: 33

Bravo AF: 0.0804

Asia WGS AF: 0.0460 AC: 158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.6
DANN	Benign	0.32
PhyloP100		0.26
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs747942; hg19: chr10-71336466;