rs76020919

Positions:

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

Variant summary

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

The ENST00000664407.1(ENSG00000227579):​n.72-62404G>T variant causes a intron, non coding transcript 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: ENST00000664407.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000664407.1	n.72-62404G>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.000241

Gnomad4 AMR AF: 0.00170

Gnomad4 ASJ AF: 0.00437

Gnomad4 EAS AF: 0.0680

Gnomad4 SAS AF: 0.0112

Gnomad4 FIN AF: 0.00165

Gnomad4 NFE AF: 0.00237

Gnomad4 OTH AF: 0.00239

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs76020919; hg19: chr1-177781293;