rs75213930

Positions:

• chr1-82659925-G-A

Variant summary

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

The ENST00000650063.1(ENSG00000233290):​n.402-3837C>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 0.0447 in 152,068 control chromosomes in the GnomAD database, including 240 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 0.045 (240 hom., cov: 32)
• Consequence: ENST00000650063.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.125

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000650063.1	n.402-3837C>T		intron_variant, non_coding_transcript_variant
	ENST00000653483.1	n.234-3837C>T		intron_variant, non_coding_transcript_variant
	ENST00000663002.1	n.94-3837C>T		intron_variant, non_coding_transcript_variant
	ENST00000702694.1	n.94-3837C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0447 AC: 6798 AN: 151950 Hom.: 240 Cov.: 32

Gnomad AFR AF: 0.00959

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.0404

Gnomad ASJ AF: 0.0755

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0226

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.0541

Gnomad NFE AF: 0.0551

Gnomad OTH AF: 0.0426

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

GnomAD4 genome AF: 0.0447 AC: 6796 AN: 152068 Hom.: 240 Cov.: 32 AF XY: 0.0490 AC XY: 3640 AN XY: 74326

Gnomad4 AFR AF: 0.00957

Gnomad4 AMR AF: 0.0404

Gnomad4 ASJ AF: 0.0755

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.0222

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.0551

Gnomad4 OTH AF: 0.0421

Alfa AF: 0.0427 Hom.: 19

Bravo AF: 0.0360

Asia WGS AF: 0.0110 AC: 38 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.88
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs75213930; hg19: chr1-83125608;