1-172977620-C-T

Variant names:

• chr1-172977620-C-T
• rs6686648
• ENST00000432694.2:n.224-26662C>T

Variant summary

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

The ENST00000432694.2(ENSG00000224000):​n.224-26662C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.98 in 152,358 control chromosomes in the GnomAD database, including 73,161 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 0.98 (73161 hom., cov: 32)
• Consequence: ENSG00000224000 ENST00000432694.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.168
• Publications: 2 publications found

Genes affected

ENSG00000224000 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.979 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000432694.2. 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
	ENSG00000224000	ENST00000432694.2	TSL:3	n.224-26662C>T		intron	N/A
	ENSG00000224000	ENST00000717048.1		n.324-86253C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.980 AC: 149173 AN: 152240 Hom.: 73109 Cov.: 32

Gnomad AFR AF: 0.980

Gnomad AMI AF: 0.968

Gnomad AMR AF: 0.971

Gnomad ASJ AF: 0.965

Gnomad EAS AF: 0.967

Gnomad SAS AF: 0.929

Gnomad FIN AF: 0.989

Gnomad MID AF: 0.987

Gnomad NFE AF: 0.986

Gnomad OTH AF: 0.978

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

GnomAD4 genome AF: 0.980 AC: 149283 AN: 152358 Hom.: 73161 Cov.: 32 AF XY: 0.978 AC XY: 72868 AN XY: 74504

African (AFR) AF: 0.980 AC: 40757 AN: 41572

American (AMR) AF: 0.972 AC: 14868 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.965 AC: 3351 AN: 3472

East Asian (EAS) AF: 0.967 AC: 5018 AN: 5190

South Asian (SAS) AF: 0.929 AC: 4482 AN: 4826

European-Finnish (FIN) AF: 0.989 AC: 10513 AN: 10630

Middle Eastern (MID) AF: 0.986 AC: 290 AN: 294

European-Non Finnish (NFE) AF: 0.986 AC: 67056 AN: 68042

Other (OTH) AF: 0.976 AC: 2065 AN: 2116

Alfa AF: 0.984 Hom.: 25488

Bravo AF: 0.980

Asia WGS AF: 0.940 AC: 3270 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.3
DANN	Benign	0.71
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs6686648; hg19: chr1-172946760;