chr10-9209716-T-G

Variant names:

• chr10-9209716-T-G
• rs1242969
• NR_120635.1:n.590-10670A>C

Variant summary

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

The NR_120635.1(LOC101928272):​n.590-10670A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 152,032 control chromosomes in the GnomAD database, including 6,268 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 0.27 (6268 hom., cov: 32)
• Consequence: LOC101928272 NR_120635.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.424

Genes affected

LOC101928272 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928272	NR_120635.1	n.590-10670A>C		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40676 AN: 151912 Hom.: 6273 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.267 AC: 40667 AN: 152032 Hom.: 6268 Cov.: 32 AF XY: 0.271 AC XY: 20173 AN XY: 74320

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.215

Gnomad4 EAS AF: 0.390

Gnomad4 SAS AF: 0.468

Gnomad4 FIN AF: 0.340

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.284

Alfa AF: 0.306 Hom.: 5325

Bravo AF: 0.251

Asia WGS AF: 0.407 AC: 1414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.4
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: rs1242969; hg19: chr10-9251679;