rs747942

chr10-69576710-T-Cchr10-69576710-T-G

Variant summary

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

The ENST00000685746.2(ENSG00000236154):n.549-273T>C variant causes a intron, non coding transcript 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: ENST00000685746.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.264

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC101929021	XR_946037.2	n.498-273T>C		intron_variant, non_coding_transcript_variant
LOC101929021	XR_428765.3	n.231-273T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000685746.2	n.549-273T>C		intron_variant, non_coding_transcript_variant
	ENST00000428753.1	n.332-273T>C		intron_variant, non_coding_transcript_variant		3
	ENST00000691761.2	n.323-278T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.240

Gnomad4 AMR AF: 0.0293

Gnomad4 ASJ AF: 0.0147

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0533

Gnomad4 FIN AF: 0.000283

Gnomad4 NFE AF: 0.00112

Gnomad4 OTH AF: 0.0583

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs747942; hg19: chr10-71336466;