6-163765645-A-G

Position:

• chr6-163765645-A-G

Variant summary

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

The ENST00000657614.1(ENSG00000235538):​n.329+6280A>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 0.341 in 152,142 control chromosomes in the GnomAD database, including 9,141 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 0.34 (9141 hom., cov: 33)
• Consequence: ENST00000657614.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.97

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.1).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.417 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
	ENST00000657614.1	n.329+6280A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51787 AN: 152024 Hom.: 9120 Cov.: 33

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.341 AC: 51861 AN: 152142 Hom.: 9141 Cov.: 33 AF XY: 0.337 AC XY: 25062 AN XY: 74374

Gnomad4 AFR AF: 0.423

Gnomad4 AMR AF: 0.297

Gnomad4 ASJ AF: 0.437

Gnomad4 EAS AF: 0.363

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.228

Gnomad4 NFE AF: 0.315

Gnomad4 OTH AF: 0.355

Alfa AF: 0.322 Hom.: 18660

Bravo AF: 0.352

Asia WGS AF: 0.313 AC: 1090 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.0030
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10945919; hg19: chr6-164186677;