rs10762264

Positions:

• chr10-69217077-G-A

Variant summary

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

The NR_120648.1(LOC101928994):​n.494-305C>T 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 0.579 in 151,978 control chromosomes in the GnomAD database, including 26,473 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 0.58 (26473 hom., cov: 32)
• Consequence: LOC101928994 NR_120648.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.964

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.658 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101928994	NR_120648.1	n.494-305C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000450995.1	n.494-305C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.579 AC: 87897 AN: 151860 Hom.: 26442 Cov.: 32

Gnomad AFR AF: 0.465

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.741

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.579 AC: 87974 AN: 151978 Hom.: 26473 Cov.: 32 AF XY: 0.578 AC XY: 42958 AN XY: 74270

Gnomad4 AFR AF: 0.465

Gnomad4 AMR AF: 0.546

Gnomad4 ASJ AF: 0.443

Gnomad4 EAS AF: 0.247

Gnomad4 SAS AF: 0.568

Gnomad4 FIN AF: 0.741

Gnomad4 NFE AF: 0.664

Gnomad4 OTH AF: 0.539

Alfa AF: 0.624 Hom.: 3784

Bravo AF: 0.554

Asia WGS AF: 0.390 AC: 1360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.45
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10762264; hg19: chr10-70976833;