rs74703854

Variant names:

• chr1-177815068-A-G
• rs74703854
• ENST00000664407.1:n.72-65314T>C

Variant summary

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

The ENST00000664407.1(ENSG00000227579):​n.72-65314T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00421 in 152,354 control chromosomes in the GnomAD database, including 8 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 0.0042 (8 hom., cov: 32)
• Consequence: ENSG00000227579 ENST00000664407.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200

Genes affected

ENSG00000227579 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0615 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000227579	ENST00000664407.1	n.72-65314T>C		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.00426 AC: 648 AN: 152236 Hom.: 8 Cov.: 32

Gnomad AFR AF: 0.000241

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00164

Gnomad ASJ AF: 0.00432

Gnomad EAS AF: 0.0674

Gnomad SAS AF: 0.0120

Gnomad FIN AF: 0.00169

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00237

Gnomad OTH AF: 0.00287

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

GnomAD4 genome AF: 0.00421 AC: 642 AN: 152354 Hom.: 8 Cov.: 32 AF XY: 0.00478 AC XY: 356 AN XY: 74502

Gnomad4 AFR AF: 0.000240

Gnomad4 AMR AF: 0.00163

Gnomad4 ASJ AF: 0.00432

Gnomad4 EAS AF: 0.0673

Gnomad4 SAS AF: 0.0112

Gnomad4 FIN AF: 0.00169

Gnomad4 NFE AF: 0.00237

Gnomad4 OTH AF: 0.00237

Alfa AF: 0.00270 Hom.: 0

Bravo AF: 0.00364

Asia WGS AF: 0.0240 AC: 82 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs74703854; hg19: chr1-177784203;