chr1-193533479-A-G

Variant names:

• chr1-193533479-A-G
• rs6692705
• ENST00000656143.2:n.153+60103A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000656143.2(ENSG00000227240):​n.153+60103A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 151,974 control chromosomes in the GnomAD database, including 21,687 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 0.52 (21687 hom., cov: 32)
• Consequence: ENSG00000227240 ENST00000656143.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.326
• Publications: 2 publications found

Genes affected

ENSG00000227240 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000656143.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000227240	ENST00000656143.2		n.153+60103A>G		intron	N/A
	ENSG00000286285	ENST00000691564.2		n.283-12569A>G		intron	N/A
	ENSG00000286285	ENST00000767304.1		n.346-12569A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.516 AC: 78401 AN: 151856 Hom.: 21679 Cov.: 32

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.734

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.634

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.516 AC: 78425 AN: 151974 Hom.: 21687 Cov.: 32 AF XY: 0.512 AC XY: 38023 AN XY: 74274

African (AFR) AF: 0.364 AC: 15092 AN: 41418

American (AMR) AF: 0.500 AC: 7637 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.678 AC: 2347 AN: 3464

East Asian (EAS) AF: 0.175 AC: 904 AN: 5168

South Asian (SAS) AF: 0.408 AC: 1966 AN: 4814

European-Finnish (FIN) AF: 0.634 AC: 6693 AN: 10560

Middle Eastern (MID) AF: 0.572 AC: 167 AN: 292

European-Non Finnish (NFE) AF: 0.615 AC: 41816 AN: 67968

Other (OTH) AF: 0.537 AC: 1135 AN: 2112

Alfa AF: 0.575 Hom.: 69235

Bravo AF: 0.494

Asia WGS AF: 0.303 AC: 1052 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.9
DANN	Benign	0.86
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs6692705; hg19: chr1-193502609;