rs2791473

Positions:

• chr1-86523026-G-A
• chr1-86523026-G-C

Variant summary

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

The XR_947556.2(LOC105378826):​n.572-189G>A 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 0.471 in 152,068 control chromosomes in the GnomAD database, including 18,944 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 0.47 (18944 hom., cov: 32)
• Consequence: LOC105378826 XR_947556.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.665

Genes affected

LOC124904210 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.575 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124904210	XR_007066206.1	n.225+4346C>T		intron_variant, non_coding_transcript_variant
LOC105378826	XR_947556.2	n.572-189G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.471 AC: 71547 AN: 151950 Hom.: 18929 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.654

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.471 AC: 71587 AN: 152068 Hom.: 18944 Cov.: 32 AF XY: 0.476 AC XY: 35358 AN XY: 74344

Gnomad4 AFR AF: 0.212

Gnomad4 AMR AF: 0.585

Gnomad4 ASJ AF: 0.513

Gnomad4 EAS AF: 0.376

Gnomad4 SAS AF: 0.471

Gnomad4 FIN AF: 0.654

Gnomad4 NFE AF: 0.577

Gnomad4 OTH AF: 0.481

Alfa AF: 0.546 Hom.: 46583

Bravo AF: 0.454

Asia WGS AF: 0.381 AC: 1324 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	2.1
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2791473; hg19: chr1-86988709;