rs6111021

Variant names:

• chr20-16293208-A-C
• rs6111021
• NM_024704.5:c.3795+19127T>G

Your query was ambiguous. Multiple possible variants found:

• chr20-16293208-A-C
• chr20-16293208-A-G
• chr20-16293208-A-T

Variant summary

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

The NM_024704.5(KIF16B):​c.3795+19127T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 151,968 control chromosomes in the GnomAD database, including 15,766 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 0.44 (15766 hom., cov: 32)
• Consequence: KIF16B NM_024704.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.430
• Publications: 3 publications found

Genes affected

KIF16B (HGNC:15869): (kinesin family member 16B) The protein encoded by this gene is a kinesin-like protein that may be involved in intracellular trafficking. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2010]

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 (EAS) allele frequency at 95% confidence interval = 0.908 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024704.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF16B	NM_024704.5	MANE Select	c.3795+19127T>G		intron	N/A	NP_078980.3
	KIF16B	NM_001199865.2		c.3642+19127T>G		intron	N/A	NP_001186794.1	A0A1B0GTU3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF16B	ENST00000354981.7	TSL:1 MANE Select	c.3795+19127T>G		intron	N/A	ENSP00000347076.2	Q96L93-1
	KIF16B	ENST00000636835.1	TSL:1	c.3642+19127T>G		intron	N/A	ENSP00000489838.1	A0A1B0GTU3
	KIF16B	ENST00000917258.1		c.3705+19127T>G		intron	N/A	ENSP00000587317.1

Frequencies

GnomAD3 genomes AF: 0.439 AC: 66653 AN: 151850 Hom.: 15734 Cov.: 32

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.930

Gnomad SAS AF: 0.711

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.439 AC: 66729 AN: 151968 Hom.: 15766 Cov.: 32 AF XY: 0.445 AC XY: 33026 AN XY: 74260

African (AFR) AF: 0.361 AC: 14971 AN: 41432

American (AMR) AF: 0.488 AC: 7454 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1683 AN: 3470

East Asian (EAS) AF: 0.930 AC: 4799 AN: 5158

South Asian (SAS) AF: 0.711 AC: 3415 AN: 4804

European-Finnish (FIN) AF: 0.378 AC: 3994 AN: 10558

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.428 AC: 29052 AN: 67954

Other (OTH) AF: 0.431 AC: 910 AN: 2110

Alfa AF: 0.427 Hom.: 7435

Bravo AF: 0.442

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.98
DANN	Benign	0.18
PhyloP100		-0.43
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6111021; hg19: chr20-16273853;