22-25197691-A-G

Variant names:

• chr22-25197691-A-G
• rs763281
• NM_001145206.2:c.*5290A>G

Variant summary

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

The NM_001145206.2(KIAA1671):​c.*5290A>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 152,044 control chromosomes in the GnomAD database, including 8,510 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 0.33 (8510 hom., cov: 32)
• Consequence: KIAA1671 NM_001145206.2 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0900
• Publications: 8 publications found

Genes affected

KIAA1671 (HGNC:29345): (KIAA1671)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIAA1671	NM_001145206.2	c.*5290A>G		downstream_gene_variant		ENST00000358431.8	NP_001138678.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIAA1671	ENST00000358431.8	c.*5290A>G		downstream_gene_variant		1	NM_001145206.2	ENSP00000351207.3
KIAA1671	ENST00000401395.1	c.*5290A>G		downstream_gene_variant		1		ENSP00000385377.1

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49623 AN: 151926 Hom.: 8482 Cov.: 32

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.327 AC: 49687 AN: 152044 Hom.: 8510 Cov.: 32 AF XY: 0.328 AC XY: 24388 AN XY: 74338

African (AFR) AF: 0.278 AC: 11540 AN: 41460

American (AMR) AF: 0.415 AC: 6346 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.292 AC: 1013 AN: 3466

East Asian (EAS) AF: 0.473 AC: 2450 AN: 5178

South Asian (SAS) AF: 0.303 AC: 1459 AN: 4816

European-Finnish (FIN) AF: 0.287 AC: 3036 AN: 10570

Middle Eastern (MID) AF: 0.373 AC: 109 AN: 292

European-Non Finnish (NFE) AF: 0.334 AC: 22732 AN: 67970

Other (OTH) AF: 0.349 AC: 736 AN: 2106

Alfa AF: 0.330 Hom.: 1804

Bravo AF: 0.341

Asia WGS AF: 0.407 AC: 1418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.9
DANN	Benign	0.58
PhyloP100		-0.090

Splicing

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

Other links and lift over

dbSNP: rs763281; hg19: chr22-25593658;