3-167860439-A-G

Variant names:

• chr3-167860439-A-G
• rs1027242
• ENST00000735796.1:n.144-3723T>C

Variant summary

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

The ENST00000735796.1(ENSG00000296043):​n.144-3723T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.57 in 151,994 control chromosomes in the GnomAD database, including 25,160 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 0.57 (25160 hom., cov: 31)
• Consequence: ENSG00000296043 ENST00000735796.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90
• Publications: 3 publications found

Genes affected

ENSG00000296043 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296043	ENST00000735796.1	n.144-3723T>C		intron_variant	Intron 1 of 3
ENSG00000296043	ENST00000735797.1	n.423+43T>C		intron_variant	Intron 3 of 5
ENSG00000296043	ENST00000735798.1	n.139-3723T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86526 AN: 151876 Hom.: 25131 Cov.: 31

Gnomad AFR AF: 0.625

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.570 AC: 86615 AN: 151994 Hom.: 25160 Cov.: 31 AF XY: 0.567 AC XY: 42104 AN XY: 74308

African (AFR) AF: 0.625 AC: 25906 AN: 41448

American (AMR) AF: 0.656 AC: 10021 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 2013 AN: 3472

East Asian (EAS) AF: 0.362 AC: 1865 AN: 5158

South Asian (SAS) AF: 0.309 AC: 1488 AN: 4814

European-Finnish (FIN) AF: 0.532 AC: 5611 AN: 10554

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.558 AC: 37930 AN: 67948

Other (OTH) AF: 0.588 AC: 1240 AN: 2110

Alfa AF: 0.554 Hom.: 102688

Bravo AF: 0.585

Asia WGS AF: 0.370 AC: 1286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.13
DANN	Benign	0.29
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs1027242; hg19: chr3-167578227;