rs7981942

Positions:

• chr13-80049211-A-C
• chr13-80049211-A-G
• chr13-80049211-A-T

Variant summary

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

The ENST00000648514.1(ENSG00000284196):​n.628-1978T>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 0.296 in 152,142 control chromosomes in the GnomAD database, including 7,765 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 0.30 (7765 hom., cov: 33)
• Consequence: ENST00000648514.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.638

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000648514.1	n.628-1978T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.296 AC: 44975 AN: 152024 Hom.: 7735 Cov.: 33

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.296 AC: 45048 AN: 152142 Hom.: 7765 Cov.: 33 AF XY: 0.300 AC XY: 22296 AN XY: 74372

Gnomad4 AFR AF: 0.309

Gnomad4 AMR AF: 0.439

Gnomad4 ASJ AF: 0.362

Gnomad4 EAS AF: 0.729

Gnomad4 SAS AF: 0.491

Gnomad4 FIN AF: 0.161

Gnomad4 NFE AF: 0.227

Gnomad4 OTH AF: 0.322

Alfa AF: 0.251 Hom.: 10473

Bravo AF: 0.319

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	15
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7981942; hg19: chr13-80623346;