rs10499012

chr6-97319715-G-Achr6-97319715-G-C

Variant summary

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

The NR_110757.1(LOC101927314):n.511+13619G>A 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 0.061 in 152,202 control chromosomes in the GnomAD database, including 1,272 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 0.061 (1272 hom., cov: 32)
• Consequence: LOC101927314 NR_110757.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.606

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927314	NR_110757.1	n.511+13619G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000656098.1	n.520+13619G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0609 AC: 9255 AN: 152086 Hom.: 1260 Cov.: 32

Gnomad AFR AF: 0.0440

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.0150

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.0757

Gnomad FIN AF: 0.0417

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00594

Gnomad OTH AF: 0.0641

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

GnomAD4 genome AF: 0.0610 AC: 9282 AN: 152202 Hom.: 1272 Cov.: 32 AF XY: 0.0684 AC XY: 5090 AN XY: 74406

Gnomad4 AFR AF: 0.0441

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.0150

Gnomad4 EAS AF: 0.502

Gnomad4 SAS AF: 0.0756

Gnomad4 FIN AF: 0.0417

Gnomad4 NFE AF: 0.00594

Gnomad4 OTH AF: 0.0639

Alfa AF: 0.0348 Hom.: 83

Bravo AF: 0.0810

Asia WGS AF: 0.249 AC: 863 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	3.1
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10499012; hg19: chr6-97767591;