chr2-38552247-G-A

Variant names:

• chr2-38552247-G-A
• rs6727476
• ENST00000737885.1:n.297-13164G>A

Variant summary

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

The ENST00000737885.1(ENSG00000296297):​n.297-13164G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 152,080 control chromosomes in the GnomAD database, including 7,312 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 0.28 (7312 hom., cov: 32)
• Consequence: ENSG00000296297 ENST00000737885.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.133
• Publications: 0 publications found

Genes affected

ENSG00000296297 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.49 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
ENSG00000296297	ENST00000737885.1	n.297-13164G>A		intron_variant	Intron 1 of 1
ENSG00000296297	ENST00000737886.1	n.351-13164G>A		intron_variant	Intron 1 of 1
ENSG00000296297	ENST00000737888.1	n.151-15525G>A		intron_variant	Intron 1 of 1
ENSG00000296331	ENST00000738305.1	n.152+9255C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42269 AN: 151962 Hom.: 7281 Cov.: 32

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.278 AC: 42333 AN: 152080 Hom.: 7312 Cov.: 32 AF XY: 0.272 AC XY: 20249 AN XY: 74356

African (AFR) AF: 0.496 AC: 20555 AN: 41438

American (AMR) AF: 0.197 AC: 3017 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 620 AN: 3472

East Asian (EAS) AF: 0.264 AC: 1369 AN: 5184

South Asian (SAS) AF: 0.180 AC: 870 AN: 4828

European-Finnish (FIN) AF: 0.132 AC: 1396 AN: 10584

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.200 AC: 13616 AN: 67972

Other (OTH) AF: 0.236 AC: 498 AN: 2114

Alfa AF: 0.240 Hom.: 2271

Bravo AF: 0.295

Asia WGS AF: 0.210 AC: 731 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.50
DANN	Benign	0.22
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs6727476; hg19: chr2-38779389;