rs713478

Variant names:

• chr9-78697204-C-A
• rs713478
• ENST00000761518.1:n.140+1937C>A

Your query was ambiguous. Multiple possible variants found:

• chr9-78697204-C-A
• chr9-78697204-C-G
• chr9-78697204-C-T

Variant summary

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

The ENST00000761518.1(ENSG00000299197):​n.140+1937C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 152,042 control chromosomes in the GnomAD database, including 5,894 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 (5894 hom., cov: 32)
• Consequence: ENSG00000299197 ENST00000761518.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.383
• Publications: 3 publications found

Genes affected

ENSG00000299197 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.379 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
ENSG00000299197	ENST00000761518.1	n.140+1937C>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38156 AN: 151924 Hom.: 5886 Cov.: 32

Gnomad AFR AF: 0.0776

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.251 AC: 38176 AN: 152042 Hom.: 5894 Cov.: 32 AF XY: 0.257 AC XY: 19129 AN XY: 74308

African (AFR) AF: 0.0775 AC: 3215 AN: 41500

American (AMR) AF: 0.354 AC: 5408 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 816 AN: 3472

East Asian (EAS) AF: 0.393 AC: 2029 AN: 5160

South Asian (SAS) AF: 0.180 AC: 868 AN: 4820

European-Finnish (FIN) AF: 0.385 AC: 4062 AN: 10540

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.304 AC: 20659 AN: 67970

Other (OTH) AF: 0.273 AC: 577 AN: 2110

Alfa AF: 0.246 Hom.: 839

Bravo AF: 0.246

Asia WGS AF: 0.276 AC: 957 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.1
DANN	Benign	0.42
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs713478; hg19: chr9-81312120;