rs1662594

Variant names:

• chr17-46915371-G-A
• rs1662594
• ENST00000750540.1:n.322G>A

Variant summary

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

The ENST00000750540.1(ENSG00000297729):​n.322G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.374 in 151,986 control chromosomes in the GnomAD database, including 10,717 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 0.37 (10717 hom., cov: 31)
• Consequence: ENSG00000297729 ENST00000750540.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.938
• Publications: 11 publications found

Genes affected

ENSG00000297729 (HGNC:):

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

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 = 0.463 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC112268191	XR_002958114.2	n.389G>A		non_coding_transcript_exon_variant	Exon 2 of 2
LRRC37A2	XM_024450773.2	c.4810-133685G>A		intron_variant	Intron 10 of 10		XP_024306541.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297729	ENST00000750540.1	n.322G>A		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000297729	ENST00000750541.1	n.359G>A		non_coding_transcript_exon_variant	Exon 2 of 2
GOSR2-DT	ENST00000715847.1	n.270-5205C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56871 AN: 151870 Hom.: 10716 Cov.: 31

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.374 AC: 56898 AN: 151986 Hom.: 10717 Cov.: 31 AF XY: 0.378 AC XY: 28079 AN XY: 74256

African (AFR) AF: 0.321 AC: 13319 AN: 41452

American (AMR) AF: 0.416 AC: 6363 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1057 AN: 3468

East Asian (EAS) AF: 0.447 AC: 2303 AN: 5156

South Asian (SAS) AF: 0.479 AC: 2300 AN: 4800

European-Finnish (FIN) AF: 0.410 AC: 4333 AN: 10556

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.381 AC: 25866 AN: 67962

Other (OTH) AF: 0.385 AC: 812 AN: 2108

Alfa AF: 0.376 Hom.: 3496

Bravo AF: 0.370

Asia WGS AF: 0.441 AC: 1536 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	1.6
DANN	Benign	0.59
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs1662594; hg19: chr17-44992737;