rs1345934

Variant names:

• chr7-137087528-A-G
• rs1345934
• ENST00000439694.6:n.477-54615T>C

Your query was ambiguous. Multiple possible variants found:

• chr7-137087528-A-G
• chr7-137087528-A-T

Variant summary

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

The ENST00000439694.6(ENSG00000234352):​n.477-54615T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 151,638 control chromosomes in the GnomAD database, including 7,679 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 0.31 (7679 hom., cov: 31)
• Consequence: ENSG00000234352 ENST00000439694.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.231
• Publications: 2 publications found

Genes affected

ENSG00000234352 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.555 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC349160	NR_046103.1	n.222-54615T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000234352	ENST00000439694.6	n.477-54615T>C		intron_variant	Intron 1 of 3	1
ENSG00000234352	ENST00000425981.2	n.222-54615T>C		intron_variant	Intron 1 of 3	2
ENSG00000234352	ENST00000586239.5	n.154-54615T>C		intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes AF: 0.307 AC: 46527 AN: 151518 Hom.: 7658 Cov.: 31

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.307 AC: 46582 AN: 151638 Hom.: 7679 Cov.: 31 AF XY: 0.312 AC XY: 23103 AN XY: 74112

African (AFR) AF: 0.341 AC: 14079 AN: 41328

American (AMR) AF: 0.403 AC: 6128 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 876 AN: 3466

East Asian (EAS) AF: 0.572 AC: 2954 AN: 5160

South Asian (SAS) AF: 0.456 AC: 2187 AN: 4798

European-Finnish (FIN) AF: 0.231 AC: 2422 AN: 10496

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.252 AC: 17121 AN: 67884

Other (OTH) AF: 0.291 AC: 612 AN: 2106

Alfa AF: 0.270 Hom.: 9228

Bravo AF: 0.321

Asia WGS AF: 0.467 AC: 1622 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.18
DANN	Benign	0.56
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs1345934; hg19: chr7-136772275;