rs2657195

Variant names:

• chr8-91547687-A-G
• rs2657195
• ENST00000521199.1:n.474-1233T>C

Variant summary

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

The ENST00000521199.1(ENSG00000253901):​n.474-1233T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 134,534 control chromosomes in the GnomAD database, including 1,863 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 (1863 hom., cov: 31)
• Consequence: ENSG00000253901 ENST00000521199.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.959
• Publications: 6 publications found

Genes affected

ENSG00000253901 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.206 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
ENSG00000253901	ENST00000521199.1	n.474-1233T>C		intron_variant	Intron 2 of 3	5
ENSG00000253901	ENST00000841363.1	n.238-1233T>C		intron_variant	Intron 1 of 3
ENSG00000253901	ENST00000841364.1	n.392-1233T>C		intron_variant	Intron 2 of 3
ENSG00000253901	ENST00000841365.1	n.130-1233T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.156 AC: 20993 AN: 134528 Hom.: 1865 Cov.: 31

Gnomad AFR AF: 0.0515

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.00266

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.195

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.156 AC: 20985 AN: 134534 Hom.: 1863 Cov.: 31 AF XY: 0.153 AC XY: 10037 AN XY: 65584

African (AFR) AF: 0.0515 AC: 1505 AN: 29208

American (AMR) AF: 0.146 AC: 2063 AN: 14118

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 416 AN: 3400

East Asian (EAS) AF: 0.00267 AC: 13 AN: 4872

South Asian (SAS) AF: 0.169 AC: 782 AN: 4622

European-Finnish (FIN) AF: 0.197 AC: 1835 AN: 9324

Middle Eastern (MID) AF: 0.190 AC: 54 AN: 284

European-Non Finnish (NFE) AF: 0.209 AC: 13784 AN: 65942

Other (OTH) AF: 0.148 AC: 276 AN: 1862

Alfa AF: 0.166 Hom.: 280

Bravo AF: 0.130

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.17
DANN	Benign	0.32
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs2657195; hg19: chr8-92559915;