rs4699748

Variant names:

• chr4-99400286-G-A
• rs4699748
• ENST00000762194.1:n.377+2547C>T

Variant summary

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

The ENST00000762194.1(ENSG00000299279):​n.377+2547C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 152,106 control chromosomes in the GnomAD database, including 1,239 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 0.13 (1239 hom., cov: 32)
• Consequence: ENSG00000299279 ENST00000762194.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0940
• Publications: 12 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=-0.58).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723576	XR_001741777.2	n.387+2547C>T		intron_variant	Intron 3 of 3
LOC102723576	XR_427569.4	n.1284+2547C>T		intron_variant	Intron 3 of 3
LOC102723576	XR_939020.3	n.1284+2547C>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299279	ENST00000762194.1	n.377+2547C>T		intron_variant	Intron 3 of 4
ENSG00000299279	ENST00000762195.1	n.249+2547C>T		intron_variant	Intron 3 of 4
ENSG00000299279	ENST00000762196.1	n.492+2547C>T		intron_variant	Intron 3 of 4
ENSG00000299279	ENST00000762197.1	n.249+2547C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19159 AN: 151988 Hom.: 1233 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.0455

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.126 AC: 19193 AN: 152106 Hom.: 1239 Cov.: 32 AF XY: 0.129 AC XY: 9562 AN XY: 74358

African (AFR) AF: 0.120 AC: 4996 AN: 41488

American (AMR) AF: 0.142 AC: 2165 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0455 AC: 158 AN: 3470

East Asian (EAS) AF: 0.142 AC: 735 AN: 5174

South Asian (SAS) AF: 0.101 AC: 486 AN: 4818

European-Finnish (FIN) AF: 0.159 AC: 1682 AN: 10590

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8657 AN: 67978

Other (OTH) AF: 0.115 AC: 243 AN: 2112

Alfa AF: 0.120 Hom.: 1903

Bravo AF: 0.124

Asia WGS AF: 0.130 AC: 452 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	7.3
DANN	Benign	0.81
PhyloP100		-0.094

Splicing

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

Other links and lift over

dbSNP: rs4699748; hg19: chr4-100321443;