rs7001819

Positions:

• chr8-11792966-T-C
• chr8-11792966-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_948962.4(LOC105379243):​n.44-4899A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 152,100 control chromosomes in the GnomAD database, including 9,394 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 0.35 (9394 hom., cov: 33)
• Consequence: LOC105379243 XR_948962.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.136

Genes affected

LOC105379243 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105379243	XR_948962.4	n.44-4899A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53225 AN: 151982 Hom.: 9388 Cov.: 33

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.350 AC: 53241 AN: 152100 Hom.: 9394 Cov.: 33 AF XY: 0.343 AC XY: 25487 AN XY: 74350

Gnomad4 AFR AF: 0.332

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.422

Gnomad4 EAS AF: 0.343

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.308

Gnomad4 NFE AF: 0.381

Gnomad4 OTH AF: 0.367

Alfa AF: 0.374 Hom.: 14394

Bravo AF: 0.350

Asia WGS AF: 0.272 AC: 941 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.8
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7001819; hg19: chr8-11650475;