rs2794256

chr6-119622238-G-Achr6-119622238-G-Cchr6-119622238-G-T

Variant summary

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

The NR_134600.1(LOC105377975):n.252+71843G>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 0.263 in 152,012 control chromosomes in the GnomAD database, including 5,485 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 0.26 (5485 hom., cov: 32)
• Consequence: LOC105377975 NR_134600.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0340

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377975	NR_134600.1	n.252+71843G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000701940.1	n.325-66787G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39905 AN: 151894 Hom.: 5490 Cov.: 32

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.263 AC: 39923 AN: 152012 Hom.: 5485 Cov.: 32 AF XY: 0.267 AC XY: 19830 AN XY: 74328

Gnomad4 AFR AF: 0.219

Gnomad4 AMR AF: 0.291

Gnomad4 ASJ AF: 0.262

Gnomad4 EAS AF: 0.133

Gnomad4 SAS AF: 0.377

Gnomad4 FIN AF: 0.356

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.256

Alfa AF: 0.270 Hom.: 2860

Bravo AF: 0.250

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.0

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2794256; hg19: chr6-119943401;