rs2025934

Positions:

• chr1-193765770-G-A

Variant summary

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

The ENST00000656143.1(ENSG00000227240):​n.200+92514G>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 0.0316 in 151,966 control chromosomes in the GnomAD database, including 101 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 0.032 (101 hom., cov: 31)
• Consequence: ENST00000656143.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.274

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0501 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124904475	XR_007066777.1	n.5235-120551G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000656143.1	n.200+92514G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0317 AC: 4813 AN: 151848 Hom.: 101 Cov.: 31

Gnomad AFR AF: 0.00929

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0213

Gnomad ASJ AF: 0.0190

Gnomad EAS AF: 0.000387

Gnomad SAS AF: 0.0253

Gnomad FIN AF: 0.0304

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0515

Gnomad OTH AF: 0.0283

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

GnomAD4 genome AF: 0.0316 AC: 4809 AN: 151966 Hom.: 101 Cov.: 31 AF XY: 0.0300 AC XY: 2232 AN XY: 74280

Gnomad4 AFR AF: 0.00927

Gnomad4 AMR AF: 0.0212

Gnomad4 ASJ AF: 0.0190

Gnomad4 EAS AF: 0.000388

Gnomad4 SAS AF: 0.0251

Gnomad4 FIN AF: 0.0304

Gnomad4 NFE AF: 0.0515

Gnomad4 OTH AF: 0.0280

Alfa AF: 0.0466 Hom.: 189

Bravo AF: 0.0292

Asia WGS AF: 0.0110 AC: 40 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.55
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2025934; hg19: chr1-193734900;