rs76020919

Variant names:

• chr1-177812158-C-A
• rs76020919
• ENST00000664407.1:n.72-62404G>T

Your query was ambiguous. Multiple possible variants found:

• chr1-177812158-C-A
• chr1-177812158-C-G

Variant summary

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

The ENST00000664407.1(ENSG00000227579):​n.72-62404G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00424 in 151,244 control chromosomes in the GnomAD database, including 9 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 (9 hom., cov: 32)
• Consequence: ENSG00000227579 ENST00000664407.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490
• Publications: 1 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0621 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.72-62404G>T		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.00428 AC: 647 AN: 151126 Hom.: 9 Cov.: 32

Gnomad AFR AF: 0.000242

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00171

Gnomad ASJ AF: 0.00437

Gnomad EAS AF: 0.0680

Gnomad SAS AF: 0.0120

Gnomad FIN AF: 0.00165

Gnomad MID AF: 0.0159

Gnomad NFE AF: 0.00237

Gnomad OTH AF: 0.00290

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

GnomAD4 genome AF: 0.00424 AC: 641 AN: 151244 Hom.: 9 Cov.: 32 AF XY: 0.00482 AC XY: 356 AN XY: 73914

African (AFR) AF: 0.000241 AC: 10 AN: 41486

American (AMR) AF: 0.00170 AC: 26 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.00437 AC: 15 AN: 3434

East Asian (EAS) AF: 0.0680 AC: 349 AN: 5134

South Asian (SAS) AF: 0.0112 AC: 54 AN: 4810

European-Finnish (FIN) AF: 0.00165 AC: 17 AN: 10320

Middle Eastern (MID) AF: 0.0171 AC: 5 AN: 292

European-Non Finnish (NFE) AF: 0.00237 AC: 160 AN: 67500

Other (OTH) AF: 0.00239 AC: 5 AN: 2094

Alfa AF: 0.00270 Hom.: 0

Bravo AF: 0.00363

Asia WGS AF: 0.0230 AC: 81 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.1
DANN	Benign	0.47
PhyloP100		-0.049

Splicing

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

Other links and lift over

dbSNP: rs76020919; hg19: chr1-177781293;