rs1557026

chr1-228195666-G-Achr1-228195666-G-C

Variant summary

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

The XR_007066917.1(LOC124904536):n.7072+899G>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 0.291 in 152,000 control chromosomes in the GnomAD database, including 6,857 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 0.29 (6857 hom., cov: 32)
• Consequence: LOC124904536 XR_007066917.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.193

Genes affected

LOC124904536 (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 (NFE) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124904536	XR_007066917.1	n.7072+899G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44200 AN: 151882 Hom.: 6849 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.291 AC: 44233 AN: 152000 Hom.: 6857 Cov.: 32 AF XY: 0.285 AC XY: 21194 AN XY: 74266

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.365

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.228

Gnomad4 FIN AF: 0.279

Gnomad4 NFE AF: 0.352

Gnomad4 OTH AF: 0.307

Alfa AF: 0.307 Hom.: 890

Bravo AF: 0.288

Asia WGS AF: 0.186 AC: 648 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	3.5
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1557026; hg19: chr1-228383367;