rs719530

Variant names:

• chr7-110250908-T-C
• rs719530
• ENST00000658032.1:n.406-69898A>G

Variant summary

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

The ENST00000658032.1(ENSG00000226965):​n.406-69898A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.585 in 151,908 control chromosomes in the GnomAD database, including 26,419 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 0.58 (26419 hom., cov: 32)
• Consequence: ENSG00000226965 ENST00000658032.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.28
• Publications: 6 publications found

Genes affected

ENSG00000226965 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.665 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
ENSG00000226965	ENST00000658032.1	n.406-69898A>G		intron_variant	Intron 4 of 5
ENSG00000226965	ENST00000667232.1	n.487-69898A>G		intron_variant	Intron 5 of 7

Frequencies

GnomAD3 genomes AF: 0.585 AC: 88790 AN: 151790 Hom.: 26387 Cov.: 32

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.585 AC: 88864 AN: 151908 Hom.: 26419 Cov.: 32 AF XY: 0.578 AC XY: 42938 AN XY: 74272

African (AFR) AF: 0.672 AC: 27839 AN: 41442

American (AMR) AF: 0.632 AC: 9633 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.609 AC: 2108 AN: 3464

East Asian (EAS) AF: 0.506 AC: 2599 AN: 5138

South Asian (SAS) AF: 0.488 AC: 2353 AN: 4822

European-Finnish (FIN) AF: 0.476 AC: 5030 AN: 10570

Middle Eastern (MID) AF: 0.555 AC: 162 AN: 292

European-Non Finnish (NFE) AF: 0.550 AC: 37374 AN: 67910

Other (OTH) AF: 0.578 AC: 1220 AN: 2110

Alfa AF: 0.568 Hom.: 64079

Bravo AF: 0.606

Asia WGS AF: 0.507 AC: 1765 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.0
DANN	Benign	0.81
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs719530; hg19: chr7-109890965;