chr6-67910027-T-A

Position:

• chr6-67910027-T-A

Variant summary

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

The ENST00000653528.1(ENSG00000287557):​n.131+20920T>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 0.0444 in 150,546 control chromosomes in the GnomAD database, including 259 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 0.044 (259 hom., cov: 29)
• Consequence: ENST00000653528.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.939

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377845	XR_942662.1	n.909-11424T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000653528.1	n.131+20920T>A		intron_variant, non_coding_transcript_variant
	ENST00000661401.1	n.121-11424T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0444 AC: 6675 AN: 150446 Hom.: 255 Cov.: 29

Gnomad AFR AF: 0.0113

Gnomad AMI AF: 0.0551

Gnomad AMR AF: 0.0959

Gnomad ASJ AF: 0.0118

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.0426

Gnomad FIN AF: 0.0222

Gnomad MID AF: 0.0414

Gnomad NFE AF: 0.0475

Gnomad OTH AF: 0.0495

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

GnomAD4 genome AF: 0.0444 AC: 6688 AN: 150546 Hom.: 259 Cov.: 29 AF XY: 0.0451 AC XY: 3315 AN XY: 73506

Gnomad4 AFR AF: 0.0113

Gnomad4 AMR AF: 0.0967

Gnomad4 ASJ AF: 0.0118

Gnomad4 EAS AF: 0.183

Gnomad4 SAS AF: 0.0423

Gnomad4 FIN AF: 0.0222

Gnomad4 NFE AF: 0.0475

Gnomad4 OTH AF: 0.0495

Alfa AF: 0.0427 Hom.: 21

Bravo AF: 0.0515

Asia WGS AF: 0.0950 AC: 328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.0
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9351685; hg19: chr6-68619919; COSMIC: COSV70884303;