rs2868371

Variant names:

• chr7-76301442-C-G
• rs2868371
• ENST00000740305.1:n.197C>G

Variant summary

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

The ENST00000740305.1(ENSG00000296557):​n.197C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 152,000 control chromosomes in the GnomAD database, including 4,511 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 0.22 (4511 hom., cov: 32)
• Consequence: ENSG00000296557 ENST00000740305.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.210
• Publications: 47 publications found

Genes affected

ENSG00000296557 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.586 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
ENSG00000296557	ENST00000740305.1	n.197C>G		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000296557	ENST00000740306.1	n.196-1160C>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.224 AC: 34040 AN: 151882 Hom.: 4508 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.604

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.224 AC: 34053 AN: 152000 Hom.: 4511 Cov.: 32 AF XY: 0.227 AC XY: 16863 AN XY: 74272

African (AFR) AF: 0.124 AC: 5163 AN: 41504

American (AMR) AF: 0.261 AC: 3972 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 808 AN: 3466

East Asian (EAS) AF: 0.603 AC: 3120 AN: 5170

South Asian (SAS) AF: 0.285 AC: 1370 AN: 4814

European-Finnish (FIN) AF: 0.204 AC: 2142 AN: 10518

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.246 AC: 16710 AN: 67974

Other (OTH) AF: 0.230 AC: 486 AN: 2112

Alfa AF: 0.229 Hom.: 520

Bravo AF: 0.228

Asia WGS AF: 0.415 AC: 1442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.44
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs2868371; hg19: chr7-75930759;