chr4-99392905-C-T

Variant names:

• chr4-99392905-C-T
• rs2032350
• ENST00000762194.1:n.378-9285G>A

Variant summary

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

The ENST00000762194.1(ENSG00000299279):​n.378-9285G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 151,768 control chromosomes in the GnomAD database, including 5,444 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 (5444 hom., cov: 32)
• Consequence: ENSG00000299279 ENST00000762194.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145
• Publications: 1 publications found

Genes affected

ENSG00000299279 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.657 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723576	XR_001741777.2	n.388-9285G>A		intron_variant	Intron 3 of 3
LOC102723576	XR_427569.4	n.1285-9285G>A		intron_variant	Intron 3 of 3
LOC102723576	XR_939020.3	n.1285-9285G>A		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299279	ENST00000762194.1	n.378-9285G>A		intron_variant	Intron 3 of 4
ENSG00000299279	ENST00000762195.1	n.250-9285G>A		intron_variant	Intron 3 of 4
ENSG00000299279	ENST00000762196.1	n.493-9285G>A		intron_variant	Intron 3 of 4
ENSG00000299279	ENST00000762197.1	n.250-9285G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37622 AN: 151650 Hom.: 5438 Cov.: 32

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.248 AC: 37652 AN: 151768 Hom.: 5444 Cov.: 32 AF XY: 0.255 AC XY: 18928 AN XY: 74170

African (AFR) AF: 0.301 AC: 12456 AN: 41370

American (AMR) AF: 0.181 AC: 2754 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 591 AN: 3468

East Asian (EAS) AF: 0.676 AC: 3501 AN: 5182

South Asian (SAS) AF: 0.467 AC: 2244 AN: 4806

European-Finnish (FIN) AF: 0.172 AC: 1808 AN: 10496

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.199 AC: 13513 AN: 67904

Other (OTH) AF: 0.233 AC: 489 AN: 2098

Alfa AF: 0.225 Hom.: 555

Bravo AF: 0.247

Asia WGS AF: 0.467 AC: 1616 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.5
DANN	Benign	0.57
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs2032350; hg19: chr4-100314062;