chr7-133101533-A-C

Variant names:

• chr7-133101533-A-C
• rs10274748
• ENST00000798409.1:n.308+898T>G

Variant summary

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

The ENST00000798409.1(ENSG00000303960):​n.308+898T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0907 in 152,194 control chromosomes in the GnomAD database, including 1,378 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 0.091 (1378 hom., cov: 33)
• Consequence: ENSG00000303960 ENST00000798409.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.296
• Publications: 0 publications found

Genes affected

ENSG00000303960 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375512	NR_133931.1	n.148+898T>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303960	ENST00000798409.1	n.308+898T>G		intron_variant	Intron 2 of 2
ENSG00000303960	ENST00000798410.1	n.150+898T>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0905 AC: 13768 AN: 152076 Hom.: 1371 Cov.: 33

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.0444

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.0460

Gnomad FIN AF: 0.0313

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.00603

Gnomad OTH AF: 0.0841

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

GnomAD4 genome AF: 0.0907 AC: 13805 AN: 152194 Hom.: 1378 Cov.: 33 AF XY: 0.0955 AC XY: 7112 AN XY: 74436

African (AFR) AF: 0.201 AC: 8355 AN: 41484

American (AMR) AF: 0.200 AC: 3064 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0444 AC: 154 AN: 3468

East Asian (EAS) AF: 0.208 AC: 1077 AN: 5174

South Asian (SAS) AF: 0.0460 AC: 222 AN: 4826

European-Finnish (FIN) AF: 0.0313 AC: 332 AN: 10622

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.00601 AC: 409 AN: 68012

Other (OTH) AF: 0.0837 AC: 177 AN: 2114

Alfa AF: 0.0128 Hom.: 22

Bravo AF: 0.110

Asia WGS AF: 0.122 AC: 422 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.43
DANN	Benign	0.81
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs10274748; hg19: chr7-132786293;