chr6-159578848-G-T

Position:

• chr6-159578848-G-T

Variant summary

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

The ENST00000656085.1(ENSG00000286533):​n.42+83738C>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 0.159 in 152,168 control chromosomes in the GnomAD database, including 2,122 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 0.16 (2122 hom., cov: 32)
• Consequence: ENST00000656085.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000656085.1	n.42+83738C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24135 AN: 152052 Hom.: 2117 Cov.: 32

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.0673

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.159 AC: 24159 AN: 152168 Hom.: 2122 Cov.: 32 AF XY: 0.159 AC XY: 11818 AN XY: 74384

Gnomad4 AFR AF: 0.242

Gnomad4 AMR AF: 0.127

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.0675

Gnomad4 SAS AF: 0.179

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.138

Alfa AF: 0.142 Hom.: 292

Bravo AF: 0.157

Asia WGS AF: 0.141 AC: 490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.38
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10455776; hg19: chr6-159999880;