chr4-104835012-G-A

Variant names:

• chr4-104835012-G-A
• rs2725769
• ENST00000515127.1:n.367-88332C>T

Variant summary

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

The ENST00000723032.1(ENSG00000248242):​n.293-88332C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 151,696 control chromosomes in the GnomAD database, including 15,875 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 0.43 (15875 hom., cov: 32)
• Consequence: ENSG00000248242 ENST00000723032.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.288
• Publications: 3 publications found

Genes affected

ENSG00000248242 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.626 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000723032.1. 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
	ENSG00000248242	ENST00000515127.1	TSL:5	n.367-88332C>T		intron	N/A
	ENSG00000248242	ENST00000723032.1		n.293-88332C>T		intron	N/A
	ENSG00000248242	ENST00000723033.1		n.571+72132C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65612 AN: 151578 Hom.: 15847 Cov.: 32

Gnomad AFR AF: 0.632

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.612

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.433 AC: 65693 AN: 151696 Hom.: 15875 Cov.: 32 AF XY: 0.442 AC XY: 32729 AN XY: 74124

African (AFR) AF: 0.632 AC: 26178 AN: 41408

American (AMR) AF: 0.473 AC: 7186 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.356 AC: 1233 AN: 3462

East Asian (EAS) AF: 0.612 AC: 3144 AN: 5136

South Asian (SAS) AF: 0.466 AC: 2241 AN: 4812

European-Finnish (FIN) AF: 0.402 AC: 4240 AN: 10542

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.298 AC: 20191 AN: 67842

Other (OTH) AF: 0.413 AC: 870 AN: 2104

Alfa AF: 0.350 Hom.: 5577

Bravo AF: 0.453

Asia WGS AF: 0.529 AC: 1838 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.47
DANN	Benign	0.19
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs2725769; hg19: chr4-105756169;