rs2903813

Variant names:

• chr7-76301472-A-G
• rs2903813
• ENST00000740305.1:n.227A>G

Variant summary

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

The ENST00000740305.1(ENSG00000296557):​n.227A>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 0.155 in 151,880 control chromosomes in the GnomAD database, including 2,049 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 0.16 (2049 hom., cov: 32)
• Consequence: ENSG00000296557 ENST00000740305.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.237
• Publications: 12 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.178 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.227A>G		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000296557	ENST00000740306.1	n.196-1130A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23599 AN: 151764 Hom.: 2050 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.0165

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.0968

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.155 AC: 23597 AN: 151880 Hom.: 2049 Cov.: 32 AF XY: 0.159 AC XY: 11770 AN XY: 74174

African (AFR) AF: 0.101 AC: 4187 AN: 41502

American (AMR) AF: 0.184 AC: 2796 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.0968 AC: 335 AN: 3462

East Asian (EAS) AF: 0.182 AC: 942 AN: 5166

South Asian (SAS) AF: 0.119 AC: 573 AN: 4814

European-Finnish (FIN) AF: 0.287 AC: 2997 AN: 10434

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11441 AN: 67972

Other (OTH) AF: 0.137 AC: 290 AN: 2112

Alfa AF: 0.159 Hom.: 5400

Bravo AF: 0.148

Asia WGS AF: 0.174 AC: 606 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	6.8
DANN	Benign	0.84
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs2903813; hg19: chr7-75930789;