rs10494686

chr1-193482710-G-C

Variant summary

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

The ENST00000691564.1(ENSG00000288950):n.171G>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 0.0805 in 152,196 control chromosomes in the GnomAD database, including 1,145 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 0.080 (1145 hom., cov: 32)
• Consequence: ENST00000691564.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124904475	XR_007066777.1	n.5234+9334G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000691564.1	n.171G>C		non_coding_transcript_exon_variant	1/2
	ENST00000656143.1	n.153+9334G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0804 AC: 12229 AN: 152078 Hom.: 1141 Cov.: 32

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0752

Gnomad ASJ AF: 0.0582

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.0533

Gnomad FIN AF: 0.00235

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.00791

Gnomad OTH AF: 0.0603

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

GnomAD4 genome AF: 0.0805 AC: 12245 AN: 152196 Hom.: 1145 Cov.: 32 AF XY: 0.0816 AC XY: 6072 AN XY: 74434

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.0751

Gnomad4 ASJ AF: 0.0582

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.0531

Gnomad4 FIN AF: 0.00235

Gnomad4 NFE AF: 0.00791

Gnomad4 OTH AF: 0.0592

Alfa AF: 0.0472 Hom.: 77

Bravo AF: 0.0954

Asia WGS AF: 0.0970 AC: 337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.70
Dann	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10494686; hg19: chr1-193451840;