rs3898608

Variant names:

• chr1-221524373-T-C
• rs3898608
• ENST00000775179.1:n.280-29714T>C

Variant summary

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

The ENST00000775179.1(ENSG00000286398):​n.280-29714T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 148,504 control chromosomes in the GnomAD database, including 6,965 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 0.29 (6965 hom., cov: 27)
• Consequence: ENSG00000286398 ENST00000775179.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.270
• Publications: 0 publications found

Genes affected

ENSG00000286398 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.403 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
ENSG00000286398	ENST00000775179.1	n.280-29714T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.295 AC: 43720 AN: 148392 Hom.: 6966 Cov.: 27

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.294 AC: 43725 AN: 148504 Hom.: 6965 Cov.: 27 AF XY: 0.299 AC XY: 21649 AN XY: 72412

African (AFR) AF: 0.210 AC: 8374 AN: 39848

American (AMR) AF: 0.337 AC: 5026 AN: 14906

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1050 AN: 3446

East Asian (EAS) AF: 0.372 AC: 1863 AN: 5012

South Asian (SAS) AF: 0.418 AC: 1924 AN: 4598

European-Finnish (FIN) AF: 0.365 AC: 3686 AN: 10094

Middle Eastern (MID) AF: 0.293 AC: 85 AN: 290

European-Non Finnish (NFE) AF: 0.309 AC: 20825 AN: 67346

Other (OTH) AF: 0.308 AC: 637 AN: 2066

Alfa AF: 0.298 Hom.: 856

Bravo AF: 0.287

Asia WGS AF: 0.317 AC: 1082 AN: 3418

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.5
DANN	Benign	0.38
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs3898608; hg19: chr1-221697715; COSMIC: COSV53384024;