rs2995073

Variant names:

• chr1-167557341-C-T
• rs2995073
• ENST00000812563.1:n.549+2269G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000812563.1(ENSG00000241666):​n.549+2269G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 151,440 control chromosomes in the GnomAD database, including 14,092 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 0.43 (14092 hom., cov: 30)
• Consequence: ENSG00000241666 ENST00000812563.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100
• Publications: 2 publications found

Genes affected

ENSG00000241666 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.478 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000241666	ENST00000812563.1	n.549+2269G>A		intron_variant	Intron 4 of 4
ENSG00000241666	ENST00000812566.1	n.293+2269G>A		intron_variant	Intron 2 of 2
ENSG00000241666	ENST00000812567.1	n.254+2269G>A		intron_variant	Intron 2 of 2
ENSG00000305739	ENST00000812696.1	n.142+999C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.429 AC: 64918 AN: 151324 Hom.: 14092 Cov.: 30

Gnomad AFR AF: 0.484

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.429 AC: 64937 AN: 151440 Hom.: 14092 Cov.: 30 AF XY: 0.424 AC XY: 31371 AN XY: 74008

African (AFR) AF: 0.484 AC: 19934 AN: 41224

American (AMR) AF: 0.474 AC: 7212 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1562 AN: 3464

East Asian (EAS) AF: 0.329 AC: 1692 AN: 5140

South Asian (SAS) AF: 0.312 AC: 1500 AN: 4812

European-Finnish (FIN) AF: 0.353 AC: 3707 AN: 10516

Middle Eastern (MID) AF: 0.483 AC: 140 AN: 290

European-Non Finnish (NFE) AF: 0.412 AC: 27950 AN: 67784

Other (OTH) AF: 0.443 AC: 928 AN: 2096

Alfa AF: 0.422 Hom.: 1643

Bravo AF: 0.446

Asia WGS AF: 0.313 AC: 1089 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.4
DANN	Benign	0.69
PhyloP100		0.010

Splicing

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

Other links and lift over

dbSNP: rs2995073; hg19: chr1-167526578;