rs6546366

Positions:

• chr2-68262535-A-C
• chr2-68262535-A-T

Variant summary

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

The ENST00000687213.1(ENSG00000289156):​n.132+10801A>C 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 0.744 in 152,080 control chromosomes in the GnomAD database, including 43,113 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 (43113 hom., cov: 33)
• Consequence: ENST00000687213.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.153

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.924 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107985892	XR_001739526.2	n.132+10801A>C		intron_variant, non_coding_transcript_variant
LOC107985892	XR_001739527.2	n.132+10801A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000687213.1	n.132+10801A>C		intron_variant, non_coding_transcript_variant
	ENST00000702914.1	n.132+10801A>C		intron_variant, non_coding_transcript_variant
	ENST00000702987.1	n.47+10886A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.744 AC: 112984 AN: 151962 Hom.: 43042 Cov.: 33

Gnomad AFR AF: 0.931

Gnomad AMI AF: 0.745

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.662

Gnomad SAS AF: 0.772

Gnomad FIN AF: 0.683

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.650

Gnomad OTH AF: 0.730

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

GnomAD4 genome AF: 0.744 AC: 113113 AN: 152080 Hom.: 43113 Cov.: 33 AF XY: 0.743 AC XY: 55199 AN XY: 74330

Gnomad4 AFR AF: 0.932

Gnomad4 AMR AF: 0.720

Gnomad4 ASJ AF: 0.710

Gnomad4 EAS AF: 0.663

Gnomad4 SAS AF: 0.772

Gnomad4 FIN AF: 0.683

Gnomad4 NFE AF: 0.650

Gnomad4 OTH AF: 0.733

Alfa AF: 0.713 Hom.: 5225

Bravo AF: 0.753

Asia WGS AF: 0.768 AC: 2634 AN: 3430

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.39
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6546366; hg19: chr2-68489667;