rs6983269

Positions:

• chr8-2741967-C-A
• chr8-2741967-C-G
• chr8-2741967-C-T

Variant summary

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

The NR_168443.1(LOC105377785):​n.538+14474C>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 0.428 in 152,034 control chromosomes in the GnomAD database, including 14,892 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 0.43 (14892 hom., cov: 33)
• Consequence: LOC105377785 NR_168443.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.202

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.58 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377785	NR_168443.1	n.538+14474C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000654515.1	n.531+14474C>A		intron_variant, non_coding_transcript_variant
	ENST00000520024.1	n.176+14474C>A		intron_variant, non_coding_transcript_variant		3
	ENST00000670600.1	n.538+14474C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.428 AC: 65087 AN: 151916 Hom.: 14878 Cov.: 33

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.364

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.428 AC: 65121 AN: 152034 Hom.: 14892 Cov.: 33 AF XY: 0.434 AC XY: 32231 AN XY: 74306

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.590

Gnomad4 ASJ AF: 0.479

Gnomad4 EAS AF: 0.365

Gnomad4 SAS AF: 0.538

Gnomad4 FIN AF: 0.485

Gnomad4 NFE AF: 0.467

Gnomad4 OTH AF: 0.453

Alfa AF: 0.317 Hom.: 846

Bravo AF: 0.430

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.1

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6983269; hg19: chr8-2599496;