rs1412337

Variant names:

• chr1-168649403-G-A
• rs1412337
• ENST00000823297.1:n.304+19335G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-168649403-G-A
• chr1-168649403-G-C
• chr1-168649403-G-T

Variant summary

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

The ENST00000823297.1(ENSG00000307075):​n.304+19335G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,216 control chromosomes in the GnomAD database, including 2,561 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 0.18 (2561 hom., cov: 33)
• Consequence: ENSG00000307075 ENST00000823297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.856
• Publications: 14 publications found

Genes affected

ENSG00000307075 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371604	XR_922259.3	n.115-8128C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307075	ENST00000823297.1	n.304+19335G>A		intron_variant	Intron 1 of 1
ENSG00000307075	ENST00000823298.1	n.485+17460G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27066 AN: 152098 Hom.: 2561 Cov.: 33

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.178 AC: 27068 AN: 152216 Hom.: 2561 Cov.: 33 AF XY: 0.181 AC XY: 13454 AN XY: 74414

African (AFR) AF: 0.135 AC: 5598 AN: 41562

American (AMR) AF: 0.148 AC: 2271 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1159 AN: 3468

East Asian (EAS) AF: 0.288 AC: 1484 AN: 5154

South Asian (SAS) AF: 0.239 AC: 1155 AN: 4824

European-Finnish (FIN) AF: 0.237 AC: 2512 AN: 10588

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.181 AC: 12298 AN: 68002

Other (OTH) AF: 0.201 AC: 424 AN: 2114

Alfa AF: 0.187 Hom.: 11840

Bravo AF: 0.171

Asia WGS AF: 0.247 AC: 857 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.044
DANN	Benign	0.76
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs1412337; hg19: chr1-168618641;