chr1-198500032-G-A

Variant names:

• chr1-198500032-G-A
• rs10922438
• ENST00000660823.1:n.327+19519C>T

Variant summary

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

The ENST00000660823.1(ENSG00000287989):​n.327+19519C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0873 in 152,070 control chromosomes in the GnomAD database, including 743 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 0.087 (743 hom., cov: 32)
• Consequence: ENSG00000287989 ENST00000660823.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.980
• Publications: 2 publications found

Genes affected

ENSG00000287989 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371677	XR_922398.3	n.260+19519C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287989	ENST00000660823.1	n.327+19519C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0871 AC: 13228 AN: 151952 Hom.: 733 Cov.: 32

Gnomad AFR AF: 0.0989

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.0931

Gnomad EAS AF: 0.0971

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.0440

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0610

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.0873 AC: 13273 AN: 152070 Hom.: 743 Cov.: 32 AF XY: 0.0900 AC XY: 6692 AN XY: 74344

African (AFR) AF: 0.0989 AC: 4100 AN: 41468

American (AMR) AF: 0.151 AC: 2311 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0931 AC: 323 AN: 3468

East Asian (EAS) AF: 0.0973 AC: 504 AN: 5180

South Asian (SAS) AF: 0.234 AC: 1127 AN: 4814

European-Finnish (FIN) AF: 0.0440 AC: 465 AN: 10574

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0610 AC: 4144 AN: 67970

Other (OTH) AF: 0.109 AC: 231 AN: 2114

Alfa AF: 0.0776 Hom.: 1002

Bravo AF: 0.0935

Asia WGS AF: 0.186 AC: 647 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.17
DANN	Benign	0.45
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs10922438; hg19: chr1-198469162;