rs1994035

Positions:

• chr8-78091416-T-C

Variant summary

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

The variant allele was found at a frequency of 0.464 in 151,664 control chromosomes in the GnomAD database, including 18,301 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 0.46 (18301 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.78091416T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.464 AC: 70253 AN: 151546 Hom.: 18262 Cov.: 31

Gnomad AFR AF: 0.712

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.464 AC: 70344 AN: 151664 Hom.: 18301 Cov.: 31 AF XY: 0.460 AC XY: 34061 AN XY: 74108

Gnomad4 AFR AF: 0.712

Gnomad4 AMR AF: 0.414

Gnomad4 ASJ AF: 0.400

Gnomad4 EAS AF: 0.504

Gnomad4 SAS AF: 0.461

Gnomad4 FIN AF: 0.329

Gnomad4 NFE AF: 0.345

Gnomad4 OTH AF: 0.448

Alfa AF: 0.412 Hom.: 2444

Bravo AF: 0.481

Asia WGS AF: 0.517 AC: 1790 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.032
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1994035; hg19: chr8-79003651; COSMIC: COSV64449526;