ENST00000715847.1:n.270-2990T>C

Variant names:

• chr17-46913156-A-G
• rs197915
• ENST00000715847.1:n.270-2990T>C

Variant summary

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

The ENST00000715847.1(GOSR2-DT):​n.270-2990T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 152,176 control chromosomes in the GnomAD database, including 11,508 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 0.39 (11508 hom., cov: 32)
• Consequence: GOSR2-DT ENST00000715847.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.739
• Publications: 7 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRRC37A2	XM_024450773.2	c.4810-135900A>G		intron_variant	Intron 10 of 10		XP_024306541.1
LOC112268191	XR_002958114.2	n.129+201A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GOSR2-DT	ENST00000715847.1	n.270-2990T>C		intron_variant	Intron 1 of 1
ENSG00000297729	ENST00000750540.1	n.101+201A>G		intron_variant	Intron 1 of 1
ENSG00000297729	ENST00000750541.1	n.99+201A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58796 AN: 152058 Hom.: 11501 Cov.: 32

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.419

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.387 AC: 58832 AN: 152176 Hom.: 11508 Cov.: 32 AF XY: 0.391 AC XY: 29066 AN XY: 74372

African (AFR) AF: 0.322 AC: 13382 AN: 41516

American (AMR) AF: 0.428 AC: 6543 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1158 AN: 3470

East Asian (EAS) AF: 0.419 AC: 2173 AN: 5180

South Asian (SAS) AF: 0.481 AC: 2318 AN: 4820

European-Finnish (FIN) AF: 0.426 AC: 4510 AN: 10576

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.401 AC: 27264 AN: 68004

Other (OTH) AF: 0.408 AC: 860 AN: 2108

Alfa AF: 0.391 Hom.: 3236

Bravo AF: 0.380

Asia WGS AF: 0.431 AC: 1502 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.21
DANN	Benign	0.20
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs197915; hg19: chr17-44990522;