rs10487946

Positions:

• chr7-69558644-A-G
• chr7-69558644-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The XR_927652.1(LOC105375346):​n.311+300A>G 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 0.0131 in 152,326 control chromosomes in the GnomAD database, including 28 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 0.013 (28 hom., cov: 32)
• Consequence: LOC105375346 XR_927652.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.30

Genes affected

LOC105375346 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0131 (2000/152326) while in subpopulation SAS AF= 0.0259 (125/4830). AF 95% confidence interval is 0.0222. There are 28 homozygotes in gnomad4. There are 947 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 28 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375346	XR_927652.1	n.311+300A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0131 AC: 2000 AN: 152208 Hom.: 28 Cov.: 32

Gnomad AFR AF: 0.00275

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.0126

Gnomad ASJ AF: 0.0671

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0259

Gnomad FIN AF: 0.00471

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0177

Gnomad OTH AF: 0.0196

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

GnomAD4 genome AF: 0.0131 AC: 2000 AN: 152326 Hom.: 28 Cov.: 32 AF XY: 0.0127 AC XY: 947 AN XY: 74488

Gnomad4 AFR AF: 0.00274

Gnomad4 AMR AF: 0.0126

Gnomad4 ASJ AF: 0.0671

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0259

Gnomad4 FIN AF: 0.00471

Gnomad4 NFE AF: 0.0177

Gnomad4 OTH AF: 0.0194

Alfa AF: 0.00501 Hom.: 1

Bravo AF: 0.0130

Asia WGS AF: 0.00866 AC: 30 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	5.8
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10487946; hg19: chr7-69023630;