chr17-46913279-C-T

Variant names:

• chr17-46913279-C-T
• rs10491148
• ENST00000715847.1:n.270-3113G>A

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

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

ENSG00000297729 (HGNC:):

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]

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRRC37A2	XM_024450773.2	c.4810-135777C>T		intron_variant	Intron 10 of 10		XP_024306541.1
LOC112268191	XR_002958114.2	n.129+324C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GOSR2-DT	ENST00000715847.1	n.270-3113G>A		intron_variant	Intron 1 of 1
ENSG00000297729	ENST00000750540.1	n.101+324C>T		intron_variant	Intron 1 of 1
ENSG00000297729	ENST00000750541.1	n.99+324C>T		intron_variant	Intron 1 of 1

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 v4.3

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

Other links and lift over

dbSNP: rs10491148; hg19: chr17-44990645;