rs739854

Variant names:

• chr7-24217698-T-C
• rs739854
• ENST00000439839.1:n.160-20669A>G

Your query was ambiguous. Multiple possible variants found:

• chr7-24217698-T-C
• chr7-24217698-T-G

Variant summary

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

The ENST00000439839.1(ENSG00000228944):​n.160-20669A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0853 in 152,174 control chromosomes in the GnomAD database, including 1,133 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 0.085 (1133 hom., cov: 31)
• Consequence: ENSG00000228944 ENST00000439839.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90
• Publications: 3 publications found

Genes affected

ENSG00000228944 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986777	XR_001745121.2	n.210-20669A>G		intron_variant	Intron 2 of 2
LOC107986777	XR_001745122.2	n.81-20669A>G		intron_variant	Intron 1 of 1
LOC107986777	XR_001745123.2	n.210-20669A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228944	ENST00000439839.1	n.160-20669A>G		intron_variant	Intron 1 of 1	5
ENSG00000228944	ENST00000718234.1	n.320-20669A>G		intron_variant	Intron 2 of 3
ENSG00000228944	ENST00000745512.1	n.342-20669A>G		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.0850 AC: 12930 AN: 152056 Hom.: 1119 Cov.: 31

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0473

Gnomad ASJ AF: 0.0141

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0172

Gnomad FIN AF: 0.0225

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0331

Gnomad OTH AF: 0.0738

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

GnomAD4 genome AF: 0.0853 AC: 12977 AN: 152174 Hom.: 1133 Cov.: 31 AF XY: 0.0821 AC XY: 6111 AN XY: 74400

African (AFR) AF: 0.228 AC: 9450 AN: 41470

American (AMR) AF: 0.0472 AC: 722 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0141 AC: 49 AN: 3468

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5170

South Asian (SAS) AF: 0.0170 AC: 82 AN: 4818

European-Finnish (FIN) AF: 0.0225 AC: 239 AN: 10622

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0331 AC: 2249 AN: 68016

Other (OTH) AF: 0.0735 AC: 155 AN: 2110

Alfa AF: 0.0339 Hom.: 46

Bravo AF: 0.0936

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.015
DANN	Benign	0.13
PhyloP100		-1.9
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs739854; hg19: chr7-24257317;