chr6-29850791-T-C

Position:

• chr6-29850791-T-C

Variant summary

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

The ENST00000647952.1(ENSG00000290870):​n.2321-162A>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 0.104 in 152,172 control chromosomes in the GnomAD database, including 1,109 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 0.10 (1109 hom., cov: 31)
• Consequence: ENST00000647952.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.819

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375010	XR_926681.2	n.207-162A>G		intron_variant, non_coding_transcript_variant
LOC105375010	XR_926680.3	n.207-162A>G		intron_variant, non_coding_transcript_variant
LOC105375010	XR_926682.3	n.206+1531A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000647952.1	n.2321-162A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15780 AN: 152054 Hom.: 1109 Cov.: 31

Gnomad AFR AF: 0.0335

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.0675

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.0183

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.0780

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.0982

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

GnomAD4 genome AF: 0.104 AC: 15773 AN: 152172 Hom.: 1109 Cov.: 31 AF XY: 0.0987 AC XY: 7345 AN XY: 74398

Gnomad4 AFR AF: 0.0335

Gnomad4 AMR AF: 0.0674

Gnomad4 ASJ AF: 0.121

Gnomad4 EAS AF: 0.0184

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.0780

Gnomad4 NFE AF: 0.162

Gnomad4 OTH AF: 0.0976

Alfa AF: 0.146 Hom.: 1410

Bravo AF: 0.0983

Asia WGS AF: 0.0630 AC: 221 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.3
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2734986; hg19: chr6-29818568;