rs4659996

Variant names:

• chr1-240682824-G-A
• rs4659996
• ENST00000739920.1:n.588-732C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-240682824-G-A
• chr1-240682824-G-C
• chr1-240682824-G-T

Variant summary

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

The ENST00000739920.1(ENSG00000296496):​n.588-732C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.557 in 151,956 control chromosomes in the GnomAD database, including 24,435 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 0.56 (24435 hom., cov: 32)
• Consequence: ENSG00000296496 ENST00000739920.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490
• Publications: 9 publications found

Genes affected

ENSG00000296496 (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 = 0.714 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000739920.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000296496	ENST00000739920.1		n.588-732C>T		intron	N/A
	ENSG00000296496	ENST00000739921.1		n.589-732C>T		intron	N/A
	ENSG00000296496	ENST00000739922.1		n.488-732C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.557 AC: 84563 AN: 151840 Hom.: 24409 Cov.: 32

Gnomad AFR AF: 0.721

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.557 AC: 84638 AN: 151956 Hom.: 24435 Cov.: 32 AF XY: 0.557 AC XY: 41362 AN XY: 74274

African (AFR) AF: 0.720 AC: 29865 AN: 41456

American (AMR) AF: 0.562 AC: 8578 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1633 AN: 3464

East Asian (EAS) AF: 0.392 AC: 2020 AN: 5156

South Asian (SAS) AF: 0.474 AC: 2275 AN: 4804

European-Finnish (FIN) AF: 0.524 AC: 5519 AN: 10524

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.488 AC: 33159 AN: 67978

Other (OTH) AF: 0.532 AC: 1122 AN: 2110

Alfa AF: 0.503 Hom.: 75401

Bravo AF: 0.566

Asia WGS AF: 0.467 AC: 1624 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	1.7
DANN	Benign	0.50
PhyloP100		-0.049

Splicing

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

Other links and lift over

dbSNP: rs4659996; hg19: chr1-240846124;