rs1608157

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC107986860 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986860	XM_017012936.2	c.572-359G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.523

Gnomad4 AMR AF: 0.513

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.489

Gnomad4 SAS AF: 0.470

Gnomad4 FIN AF: 0.580

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.441

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1608157; hg19: chr7-150247024;