1-177908844-T-C

Variant names:

• chr1-177908844-T-C
• rs604388
• ENST00000664407.1:n.71+11238A>G

Variant summary

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

The ENST00000664407.1(ENSG00000227579):​n.71+11238A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 152,046 control chromosomes in the GnomAD database, including 10,125 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 0.36 (10125 hom., cov: 32)
• Consequence: ENSG00000227579 ENST00000664407.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162
• 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.575 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000664407.1. 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	ENST00000664407.1		n.71+11238A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54257 AN: 151928 Hom.: 10115 Cov.: 32

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.593

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.357 AC: 54296 AN: 152046 Hom.: 10125 Cov.: 32 AF XY: 0.360 AC XY: 26749 AN XY: 74330

African (AFR) AF: 0.409 AC: 16945 AN: 41456

American (AMR) AF: 0.394 AC: 6015 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.242 AC: 840 AN: 3470

East Asian (EAS) AF: 0.593 AC: 3069 AN: 5176

South Asian (SAS) AF: 0.272 AC: 1312 AN: 4816

European-Finnish (FIN) AF: 0.345 AC: 3648 AN: 10564

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.315 AC: 21395 AN: 67974

Other (OTH) AF: 0.321 AC: 677 AN: 2112

Alfa AF: 0.327 Hom.: 1090

Bravo AF: 0.368

Asia WGS AF: 0.384 AC: 1332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.3
DANN	Benign	0.41
PhyloP100		-0.16

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: rs604388;

hg19: chr1-177877979;