rs1322199

Positions:

• chr6-165012028-G-A

Variant summary

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

The ENST00000667740.1(ENSG00000287877):​n.269+32711G>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 0.74 in 152,118 control chromosomes in the GnomAD database, including 41,776 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 0.74 (41776 hom., cov: 32)
• Consequence: ENST00000667740.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.81 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
	ENST00000667740.1	n.269+32711G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.740 AC: 112452 AN: 152000 Hom.: 41749 Cov.: 32

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.718

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.812

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.710

Gnomad OTH AF: 0.726

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

GnomAD4 genome AF: 0.740 AC: 112530 AN: 152118 Hom.: 41776 Cov.: 32 AF XY: 0.744 AC XY: 55328 AN XY: 74350

Gnomad4 AFR AF: 0.776

Gnomad4 AMR AF: 0.718

Gnomad4 ASJ AF: 0.717

Gnomad4 EAS AF: 0.707

Gnomad4 SAS AF: 0.832

Gnomad4 FIN AF: 0.812

Gnomad4 NFE AF: 0.710

Gnomad4 OTH AF: 0.725

Alfa AF: 0.723 Hom.: 31347

Bravo AF: 0.731

Asia WGS AF: 0.720 AC: 2503 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.0060
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1322199; hg19: chr6-165425517;