rs1608157

Variant names:

• chr7-150549936-C-G
• rs1608157
• XM_017012936.2:c.572-359G>C

Your query was ambiguous. Multiple possible variants found:

• chr7-150549936-C-G
• chr7-150549936-C-T

Variant summary

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

The XM_017012936.2(LOC107986860):​c.572-359G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 151,952 control chromosomes in the GnomAD database, including 18,419 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 0.49 (18419 hom., cov: 32)
• Consequence: LOC107986860 XM_017012936.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.980
• Publications: 7 publications found

Genes affected

LOC107986860 (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 = 0.517 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.490 AC: 74343 AN: 151836 Hom.: 18403 Cov.: 32

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.580

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.490 AC: 74411 AN: 151952 Hom.: 18419 Cov.: 32 AF XY: 0.496 AC XY: 36809 AN XY: 74280

African (AFR) AF: 0.523 AC: 21643 AN: 41410

American (AMR) AF: 0.513 AC: 7832 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1724 AN: 3470

East Asian (EAS) AF: 0.489 AC: 2532 AN: 5176

South Asian (SAS) AF: 0.470 AC: 2268 AN: 4826

European-Finnish (FIN) AF: 0.580 AC: 6120 AN: 10550

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.453 AC: 30769 AN: 67946

Other (OTH) AF: 0.441 AC: 928 AN: 2106

Alfa AF: 0.335 Hom.: 861

Bravo AF: 0.488

Asia WGS AF: 0.475 AC: 1647 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.67
DANN	Benign	0.36
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs1608157; hg19: chr7-150247024;