rs1412337

Positions:

• chr1-168649403-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_922259.3(LOC105371604):​n.115-8128C>T variant causes a intron, non coding transcript 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: LOC105371604 XR_922259.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.856

Genes affected

LOC105371604 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105371604	XR_922259.3	n.115-8128C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.288

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.237

Gnomad4 NFE AF: 0.181

Gnomad4 OTH AF: 0.201

Alfa AF: 0.189 Hom.: 6089

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1412337; hg19: chr1-168618641;