rs1983722

Positions:

• chr6-93450974-G-A

Variant summary

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

The ENST00000668367.1(ENSG00000287683):​n.151+33873G>A 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 0.0853 in 151,910 control chromosomes in the GnomAD database, including 683 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 0.085 (683 hom., cov: 31)
• Consequence: ENST00000668367.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.179

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 (NFE) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377899	XR_001744262.2	n.1220+3338G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000668367.1	n.151+33873G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0854 AC: 12960 AN: 151794 Hom.: 683 Cov.: 31

Gnomad AFR AF: 0.0263

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.0973

Gnomad ASJ AF: 0.0309

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.0909

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.0717

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

GnomAD4 genome AF: 0.0853 AC: 12957 AN: 151910 Hom.: 683 Cov.: 31 AF XY: 0.0872 AC XY: 6476 AN XY: 74248

Gnomad4 AFR AF: 0.0263

Gnomad4 AMR AF: 0.0971

Gnomad4 ASJ AF: 0.0309

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.0910

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.0714

Alfa AF: 0.104 Hom.: 422

Bravo AF: 0.0780

Asia WGS AF: 0.0920 AC: 325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.96
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1983722; hg19: chr6-94160692;