rs13056641

Positions:

• chr22-25024825-G-A

Variant summary

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

The NM_001145206.2(KIAA1671):​c.-207-808G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 152,076 control chromosomes in the GnomAD database, including 2,195 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 0.15 (2195 hom., cov: 31)
• Consequence: KIAA1671 NM_001145206.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.863

Genes affected

KIAA1671 (HGNC:29345): (KIAA1671)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIAA1671	NM_001145206.2	c.-207-808G>A		intron_variant		ENST00000358431.8	NP_001138678.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIAA1671	ENST00000358431.8	c.-207-808G>A		intron_variant		1	NM_001145206.2	ENSP00000351207
KIAA1671	ENST00000406486.8	c.-207-808G>A		intron_variant		5		ENSP00000385152

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22890 AN: 151958 Hom.: 2197 Cov.: 31

Gnomad AFR AF: 0.0359

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.150 AC: 22881 AN: 152076 Hom.: 2195 Cov.: 31 AF XY: 0.149 AC XY: 11098 AN XY: 74320

Gnomad4 AFR AF: 0.0358

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.244

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.220

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.161

Alfa AF: 0.189 Hom.: 1660

Bravo AF: 0.139

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.087
DANN	Benign	0.64

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs13056641; hg19: chr22-25420792;