6-26190519-G-A

Position:

• chr6-26190519-G-A

Variant summary

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

The ENST00000707189.1(ENSG00000291336):​n.999+66348G>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 0.106 in 152,126 control chromosomes in the GnomAD database, including 911 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 0.11 (911 hom., cov: 31)
• Consequence: ENST00000707189.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000707189.1	n.999+66348G>A		intron_variant, non_coding_transcript_variant
	ENST00000707191.1	n.1000+32398G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16118 AN: 152008 Hom.: 914 Cov.: 31

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.0851

Gnomad ASJ AF: 0.0706

Gnomad EAS AF: 0.0522

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0970

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.106 AC: 16126 AN: 152126 Hom.: 911 Cov.: 31 AF XY: 0.107 AC XY: 7940 AN XY: 74384

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.0850

Gnomad4 ASJ AF: 0.0706

Gnomad4 EAS AF: 0.0527

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.0971

Gnomad4 OTH AF: 0.108

Alfa AF: 0.0995 Hom.: 1020

Bravo AF: 0.103

Asia WGS AF: 0.0890 AC: 308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.71
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11753837; hg19: chr6-26190747;