1-170861504-A-G

Variant names:

• chr1-170861504-A-G
• rs983215
• ENST00000664920.1:n.682-53900T>C

Variant summary

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

The ENST00000664920.1(ENSG00000231424):​n.682-53900T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 152,018 control chromosomes in the GnomAD database, including 18,102 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 0.48 (18102 hom., cov: 32)
• Consequence: ENSG00000231424 ENST00000664920.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.100
• Publications: 3 publications found

Genes affected

ENSG00000231424 (HGNC:40240):

ENSG00000295370 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.637 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
ENSG00000231424	ENST00000664920.1	n.682-53900T>C		intron_variant	Intron 4 of 5
ENSG00000231424	ENST00000669750.1	n.534-53900T>C		intron_variant	Intron 3 of 4
ENSG00000231424	ENST00000670085.1	n.372-53900T>C		intron_variant	Intron 2 of 3
ENSG00000295370	ENST00000729641.1	n.92+4617A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72921 AN: 151902 Hom.: 18080 Cov.: 32

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.636

Gnomad SAS AF: 0.655

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.480 AC: 72982 AN: 152018 Hom.: 18102 Cov.: 32 AF XY: 0.488 AC XY: 36251 AN XY: 74296

African (AFR) AF: 0.362 AC: 15013 AN: 41462

American (AMR) AF: 0.548 AC: 8358 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.574 AC: 1987 AN: 3464

East Asian (EAS) AF: 0.636 AC: 3285 AN: 5168

South Asian (SAS) AF: 0.656 AC: 3156 AN: 4812

European-Finnish (FIN) AF: 0.509 AC: 5379 AN: 10566

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.502 AC: 34094 AN: 67976

Other (OTH) AF: 0.501 AC: 1055 AN: 2106

Alfa AF: 0.466 Hom.: 2600

Bravo AF: 0.477

Asia WGS AF: 0.585 AC: 2035 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	6.6
DANN	Benign	0.79
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs983215; hg19: chr1-170830645;