rs7113470

Variant names:

• chr11-80322759-C-G
• rs7113470
• ENST00000532605.1:n.79-633G>C

Your query was ambiguous. Multiple possible variants found:

• chr11-80322759-C-G
• chr11-80322759-C-T

Variant summary

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

The ENST00000532605.1(ENSG00000254434):​n.79-633G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0478 in 152,046 control chromosomes in the GnomAD database, including 877 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 0.048 (877 hom., cov: 32)
• Consequence: ENSG00000254434 ENST00000532605.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261
• Publications: 2 publications found

Genes affected

ENSG00000254434 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.365 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
ENSG00000254434	ENST00000532605.1	n.79-633G>C		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.0477 AC: 7254 AN: 151928 Hom.: 874 Cov.: 32

Gnomad AFR AF: 0.0300

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.0254

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.0640

Gnomad FIN AF: 0.00453

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00357

Gnomad OTH AF: 0.0455

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

GnomAD4 genome AF: 0.0478 AC: 7264 AN: 152046 Hom.: 877 Cov.: 32 AF XY: 0.0538 AC XY: 4001 AN XY: 74300

African (AFR) AF: 0.0299 AC: 1242 AN: 41494

American (AMR) AF: 0.216 AC: 3293 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.0254 AC: 88 AN: 3468

East Asian (EAS) AF: 0.379 AC: 1941 AN: 5120

South Asian (SAS) AF: 0.0643 AC: 310 AN: 4822

European-Finnish (FIN) AF: 0.00453 AC: 48 AN: 10602

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.00357 AC: 243 AN: 67978

Other (OTH) AF: 0.0464 AC: 98 AN: 2112

Alfa AF: 0.00259 Hom.: 2

Bravo AF: 0.0658

Asia WGS AF: 0.199 AC: 691 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.1
DANN	Benign	0.45
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs7113470; hg19: chr11-80033803;