rs1207739

Variant names:

• chr7-97030880-G-A
• rs1207739
• ENST00000737642.1:n.392+3141G>A

Your query was ambiguous. Multiple possible variants found:

• chr7-97030880-G-A
• chr7-97030880-G-T

Variant summary

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

The ENST00000737642.1(ENSG00000296253):​n.392+3141G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0574 in 152,282 control chromosomes in the GnomAD database, including 328 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 0.057 (328 hom., cov: 33)
• Consequence: ENSG00000296253 ENST00000737642.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.543
• Publications: 2 publications found

Genes affected

ENSG00000296253 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0806 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
ENSG00000296253	ENST00000737642.1	n.392+3141G>A		intron_variant	Intron 2 of 3
ENSG00000296253	ENST00000737643.1	n.172+3141G>A		intron_variant	Intron 1 of 1
ENSG00000296279	ENST00000737781.1	n.101-3110C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0574 AC: 8738 AN: 152164 Hom.: 328 Cov.: 33

Gnomad AFR AF: 0.0143

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.0526

Gnomad ASJ AF: 0.0625

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0872

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0776

Gnomad OTH AF: 0.0584

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

GnomAD4 genome AF: 0.0574 AC: 8738 AN: 152282 Hom.: 328 Cov.: 33 AF XY: 0.0583 AC XY: 4342 AN XY: 74454

African (AFR) AF: 0.0142 AC: 592 AN: 41572

American (AMR) AF: 0.0525 AC: 803 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0625 AC: 217 AN: 3472

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5188

South Asian (SAS) AF: 0.0875 AC: 422 AN: 4824

European-Finnish (FIN) AF: 0.107 AC: 1138 AN: 10586

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0776 AC: 5278 AN: 68028

Other (OTH) AF: 0.0578 AC: 122 AN: 2112

Alfa AF: 0.0688 Hom.: 820

Bravo AF: 0.0507

Asia WGS AF: 0.0330 AC: 116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.87
DANN	Benign	0.60
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs1207739; hg19: chr7-96660192;