ENST00000820624.1:n.89-824T>G

Variant names:

• chr7-107862996-A-C
• rs4598195
• ENST00000820624.1:n.89-824T>G

Variant summary

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

The ENST00000820624.1(ENSG00000306740):​n.89-824T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 152,132 control chromosomes in the GnomAD database, including 9,662 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 0.34 (9662 hom., cov: 32)
• Consequence: ENSG00000306740 ENST00000820624.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.192
• Publications: 41 publications found

Genes affected

ENSG00000306740 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375444	XR_927850.3	n.41-821T>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306740	ENST00000820624.1	n.89-824T>G		intron_variant	Intron 1 of 2
ENSG00000306740	ENST00000820625.1	n.77-821T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51707 AN: 152012 Hom.: 9658 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.340 AC: 51712 AN: 152132 Hom.: 9662 Cov.: 32 AF XY: 0.339 AC XY: 25202 AN XY: 74378

African (AFR) AF: 0.182 AC: 7562 AN: 41518

American (AMR) AF: 0.362 AC: 5535 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.408 AC: 1416 AN: 3472

East Asian (EAS) AF: 0.343 AC: 1773 AN: 5166

South Asian (SAS) AF: 0.289 AC: 1394 AN: 4824

European-Finnish (FIN) AF: 0.388 AC: 4100 AN: 10564

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.421 AC: 28643 AN: 67986

Other (OTH) AF: 0.340 AC: 717 AN: 2110

Alfa AF: 0.388 Hom.: 36911

Bravo AF: 0.332

Asia WGS AF: 0.328 AC: 1139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	8.9
DANN	Benign	0.68
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs4598195; hg19: chr7-107503441;