rs4598195

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000820624.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306740	ENST00000820624.1		n.89-824T>G		intron	N/A
	ENSG00000306740	ENST00000820625.1		n.77-821T>G		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4598195;

hg19: chr7-107503441;