rs711513

Variant names:

• chr7-109728712-A-G
• rs711513
• ENST00000830489.1:n.196-12124T>C

Variant summary

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

The ENST00000830489.1(ENSG00000308019):​n.196-12124T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 151,866 control chromosomes in the GnomAD database, including 9,349 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 0.35 (9349 hom., cov: 32)
• Consequence: ENSG00000308019 ENST00000830489.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.233
• Publications: 3 publications found

Genes affected

ENSG00000308019 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.36 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
ENSG00000308019	ENST00000830489.1	n.196-12124T>C		intron_variant	Intron 2 of 3
ENSG00000308019	ENST00000830490.1	n.184-12124T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52622 AN: 151746 Hom.: 9340 Cov.: 32

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.410

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.347 AC: 52665 AN: 151866 Hom.: 9349 Cov.: 32 AF XY: 0.345 AC XY: 25591 AN XY: 74192

African (AFR) AF: 0.365 AC: 15148 AN: 41462

American (AMR) AF: 0.247 AC: 3766 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.442 AC: 1533 AN: 3472

East Asian (EAS) AF: 0.230 AC: 1190 AN: 5176

South Asian (SAS) AF: 0.335 AC: 1614 AN: 4818

European-Finnish (FIN) AF: 0.384 AC: 4047 AN: 10542

Middle Eastern (MID) AF: 0.428 AC: 125 AN: 292

European-Non Finnish (NFE) AF: 0.355 AC: 24055 AN: 67818

Other (OTH) AF: 0.345 AC: 728 AN: 2108

Alfa AF: 0.348 Hom.: 22302

Bravo AF: 0.333

Asia WGS AF: 0.293 AC: 1015 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.64
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs711513; hg19: chr7-109368769;