rs10491148

Variant names:

• chr17-46913279-C-T
• rs10491148
• XM_024450773.2:c.4810-135777C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000715847.1(GOSR2-DT):​n.270-3113G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0337 in 152,330 control chromosomes in the GnomAD database, including 165 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 0.034 (165 hom., cov: 32)
• Consequence: GOSR2-DT ENST00000715847.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0120
• Publications: 1 publications found

Genes affected

LRRC37A2 (HGNC:32404): (leucine rich repeat containing 37 member A2) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

GOSR2-DT (HGNC:55346): (GOSR2 divergent transcript)

ENSG00000297729 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0804 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715847.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GOSR2-DT	ENST00000715847.1		n.270-3113G>A		intron	N/A
	ENSG00000297729	ENST00000750540.1		n.101+324C>T		intron	N/A
	ENSG00000297729	ENST00000750541.1		n.99+324C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0337 AC: 5125 AN: 152212 Hom.: 165 Cov.: 32

Gnomad AFR AF: 0.0829

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.0220

Gnomad ASJ AF: 0.0300

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.00310

Gnomad FIN AF: 0.0127

Gnomad MID AF: 0.0350

Gnomad NFE AF: 0.0139

Gnomad OTH AF: 0.0363

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

GnomAD4 genome AF: 0.0337 AC: 5126 AN: 152330 Hom.: 165 Cov.: 32 AF XY: 0.0327 AC XY: 2433 AN XY: 74492

African (AFR) AF: 0.0828 AC: 3439 AN: 41558

American (AMR) AF: 0.0220 AC: 336 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0300 AC: 104 AN: 3470

East Asian (EAS) AF: 0.000385 AC: 2 AN: 5190

South Asian (SAS) AF: 0.00290 AC: 14 AN: 4832

European-Finnish (FIN) AF: 0.0127 AC: 135 AN: 10626

Middle Eastern (MID) AF: 0.0377 AC: 11 AN: 292

European-Non Finnish (NFE) AF: 0.0139 AC: 946 AN: 68030

Other (OTH) AF: 0.0359 AC: 76 AN: 2116

Alfa AF: 0.0240 Hom.: 25

Bravo AF: 0.0371

Asia WGS AF: 0.00577 AC: 20 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.64
PhyloP100		-0.012

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10491148;

hg19: chr17-44990645;