7-69558644-A-G

Variant names:

• chr7-69558644-A-G
• rs10487946
• XR_927652.1:n.311+300A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The XR_927652.1(LOC105375346):​n.311+300A>G variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.30
• Publications: 1 publications found

Genes affected

LOC105375346 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 28 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375346	XR_927652.1	n.311+300A>G		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.00274 AC: 114 AN: 41576

American (AMR) AF: 0.0126 AC: 192 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0671 AC: 233 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5194

South Asian (SAS) AF: 0.0259 AC: 125 AN: 4830

European-Finnish (FIN) AF: 0.00471 AC: 50 AN: 10620

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0177 AC: 1202 AN: 68020

Other (OTH) AF: 0.0194 AC: 41 AN: 2112

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
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs10487946; hg19: chr7-69023630;