rs7798431

Variant names:

• chr7-25821192-G-A
• rs7798431
• ENST00000812174.1:n.297+27734C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-25821192-G-A
• chr7-25821192-G-C

Variant summary

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

The ENST00000812174.1(ENSG00000286725):​n.297+27734C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 152,050 control chromosomes in the GnomAD database, including 4,855 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 0.25 (4855 hom., cov: 32)
• Consequence: ENSG00000286725 ENST00000812174.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02
• Publications: 13 publications found

Genes affected

ENSG00000286725 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.459 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
ENSG00000286725	ENST00000812174.1	n.297+27734C>T		intron_variant	Intron 2 of 4
ENSG00000286725	ENST00000812175.1	n.280+27734C>T		intron_variant	Intron 2 of 5
ENSG00000286725	ENST00000812176.1	n.297+27734C>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37269 AN: 151932 Hom.: 4853 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.441

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.245 AC: 37305 AN: 152050 Hom.: 4855 Cov.: 32 AF XY: 0.253 AC XY: 18788 AN XY: 74346

African (AFR) AF: 0.195 AC: 8103 AN: 41472

American (AMR) AF: 0.215 AC: 3279 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 750 AN: 3470

East Asian (EAS) AF: 0.441 AC: 2282 AN: 5174

South Asian (SAS) AF: 0.475 AC: 2289 AN: 4816

European-Finnish (FIN) AF: 0.292 AC: 3081 AN: 10566

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.247 AC: 16759 AN: 67962

Other (OTH) AF: 0.252 AC: 531 AN: 2106

Alfa AF: 0.228 Hom.: 2731

Bravo AF: 0.233

Asia WGS AF: 0.415 AC: 1438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	6.1
DANN	Benign	0.74
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs7798431; hg19: chr7-25860812;