rs272071

Variant names:

• chr2-115848999-T-G
• rs272071
• ENST00000668438.1:n.467-13569A>C

Variant summary

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

The ENST00000668438.1(ENSG00000287451):​n.467-13569A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.706 in 151,968 control chromosomes in the GnomAD database, including 38,176 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 0.71 (38176 hom., cov: 31)
• Consequence: ENSG00000287451 ENST00000668438.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0680
• Publications: 1 publications found

Genes affected

ENSG00000287451 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.75 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
ENSG00000287451	ENST00000668438.1	n.467-13569A>C		intron_variant	Intron 2 of 2
ENSG00000287451	ENST00000773149.1	n.226-11418A>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.706 AC: 107262 AN: 151850 Hom.: 38145 Cov.: 31

Gnomad AFR AF: 0.651

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.761

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.732

Gnomad SAS AF: 0.666

Gnomad FIN AF: 0.774

Gnomad MID AF: 0.574

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.715

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

GnomAD4 genome AF: 0.706 AC: 107340 AN: 151968 Hom.: 38176 Cov.: 31 AF XY: 0.708 AC XY: 52566 AN XY: 74270

African (AFR) AF: 0.651 AC: 26975 AN: 41450

American (AMR) AF: 0.761 AC: 11628 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.702 AC: 2434 AN: 3468

East Asian (EAS) AF: 0.732 AC: 3749 AN: 5124

South Asian (SAS) AF: 0.664 AC: 3195 AN: 4810

European-Finnish (FIN) AF: 0.774 AC: 8171 AN: 10560

Middle Eastern (MID) AF: 0.562 AC: 163 AN: 290

European-Non Finnish (NFE) AF: 0.720 AC: 48959 AN: 67970

Other (OTH) AF: 0.717 AC: 1512 AN: 2110

Alfa AF: 0.711 Hom.: 32422

Bravo AF: 0.703

Asia WGS AF: 0.676 AC: 2353 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	15
DANN	Benign	0.67
PhyloP100		-0.068

Splicing

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

Other links and lift over

dbSNP: rs272071; hg19: chr2-116606575;