chr7-98483662-T-C

Variant names:

• chr7-98483662-T-C
• rs1472272
• ENST00000799996.1:n.59+12774T>C

Variant summary

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

The ENST00000799996.1(ENSG00000304141):​n.59+12774T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 151,972 control chromosomes in the GnomAD database, including 2,872 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 0.19 (2872 hom., cov: 31)
• Consequence: ENSG00000304141 ENST00000799996.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51
• Publications: 3 publications found

Genes affected

ENSG00000304141 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.322 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
ENSG00000304141	ENST00000799996.1	n.59+12774T>C		intron_variant	Intron 1 of 3
ENSG00000304141	ENST00000799997.1	n.47+12774T>C		intron_variant	Intron 1 of 5
ENSG00000304141	ENST00000799998.1	n.39+12774T>C		intron_variant	Intron 1 of 3
ENSG00000304141	ENST00000799999.1	n.153+12774T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28274 AN: 151854 Hom.: 2871 Cov.: 31

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.186 AC: 28298 AN: 151972 Hom.: 2872 Cov.: 31 AF XY: 0.188 AC XY: 13952 AN XY: 74276

African (AFR) AF: 0.262 AC: 10869 AN: 41434

American (AMR) AF: 0.146 AC: 2232 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 760 AN: 3468

East Asian (EAS) AF: 0.170 AC: 875 AN: 5154

South Asian (SAS) AF: 0.336 AC: 1613 AN: 4802

European-Finnish (FIN) AF: 0.112 AC: 1189 AN: 10570

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10088 AN: 67968

Other (OTH) AF: 0.190 AC: 400 AN: 2102

Alfa AF: 0.166 Hom.: 1226

Bravo AF: 0.189

Asia WGS AF: 0.236 AC: 819 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.67
DANN	Benign	0.48
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1472272; hg19: chr7-98112974;