rs1389240

Variant names:

• chr7-156260104-G-A
• rs1389240

Your query was ambiguous. Multiple possible variants found:

• chr7-156260104-G-A
• chr7-156260104-G-T

Variant summary

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

The variant allele was found at a frequency of 0.539 in 152,084 control chromosomes in the GnomAD database, including 22,324 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 0.54 (22324 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.275
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.576 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

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81859 AN: 151966 Hom.: 22305 Cov.: 32

Gnomad AFR AF: 0.475

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.539 AC: 81925 AN: 152084 Hom.: 22324 Cov.: 32 AF XY: 0.540 AC XY: 40136 AN XY: 74350

African (AFR) AF: 0.475 AC: 19714 AN: 41486

American (AMR) AF: 0.577 AC: 8820 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.527 AC: 1829 AN: 3472

East Asian (EAS) AF: 0.320 AC: 1655 AN: 5170

South Asian (SAS) AF: 0.567 AC: 2730 AN: 4818

European-Finnish (FIN) AF: 0.561 AC: 5928 AN: 10570

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.581 AC: 39473 AN: 67978

Other (OTH) AF: 0.547 AC: 1152 AN: 2106

Alfa AF: 0.541 Hom.: 6707

Bravo AF: 0.532

Asia WGS AF: 0.456 AC: 1584 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.1
DANN	Benign	0.59
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs1389240; hg19: chr7-156052798;