1-177652066-T-C

Variant names:

• chr1-177652066-T-C
• rs1572511
• ENST00000438575.7:n.92-75116A>G

Variant summary

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

The ENST00000438575.7(ENSG00000227579):​n.92-75116A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.468 in 152,032 control chromosomes in the GnomAD database, including 17,029 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 0.47 (17029 hom., cov: 32)
• Consequence: ENSG00000227579 ENST00000438575.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.463
• Publications: 4 publications found

Genes affected

ENSG00000227579 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.507 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000438575.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000227579	ENST00000438575.7	TSL:3	n.92-75116A>G		intron	N/A
	ENSG00000227579	ENST00000663166.1		n.277-75116A>G		intron	N/A
	ENSG00000227579	ENST00000663978.1		n.180-75116A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.468 AC: 71023 AN: 151914 Hom.: 17001 Cov.: 32

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.468 AC: 71096 AN: 152032 Hom.: 17029 Cov.: 32 AF XY: 0.463 AC XY: 34376 AN XY: 74312

African (AFR) AF: 0.452 AC: 18719 AN: 41448

American (AMR) AF: 0.408 AC: 6235 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 2005 AN: 3468

East Asian (EAS) AF: 0.174 AC: 902 AN: 5180

South Asian (SAS) AF: 0.388 AC: 1871 AN: 4822

European-Finnish (FIN) AF: 0.474 AC: 5004 AN: 10560

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.511 AC: 34763 AN: 67966

Other (OTH) AF: 0.485 AC: 1024 AN: 2112

Alfa AF: 0.497 Hom.: 23828

Bravo AF: 0.465

Asia WGS AF: 0.317 AC: 1106 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.2
DANN	Benign	0.53
PhyloP100		0.46

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1572511;

hg19: chr1-177621201;