11-65726789-G-T

Variant names:

• chr11-65726789-G-T
• rs478304
• ENST00000744235.1:n.778+444C>A

Variant summary

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

The ENST00000744235.1(ENSG00000297007):​n.778+444C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 165,696 control chromosomes in the GnomAD database, including 23,896 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 0.54 (22301 hom., cov: 32)
  • Exomes 𝑓: 0.46 (1595 hom.)
• Consequence: ENSG00000297007 ENST00000744235.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 17 publications found

Genes affected

ENSG00000297007 (HGNC:):

KRT8P26 (HGNC:33378): (keratin 8 pseudogene 26)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.596 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000744235.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297007	ENST00000744235.1		n.778+444C>A		intron	N/A
	ENSG00000297007	ENST00000744236.1		n.1067+131C>A		intron	N/A
	ENSG00000297007	ENST00000744237.1		n.902+131C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81453 AN: 151954 Hom.: 22274 Cov.: 32

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.561

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.530

Gnomad OTH AF: 0.542

GnomAD4 exome AF: 0.456 AC: 6211 AN: 13624 Hom.: 1595 AF XY: 0.431 AC XY: 2962 AN XY: 6872

African (AFR) AF: 0.557 AC: 97 AN: 174

American (AMR) AF: 0.651 AC: 483 AN: 742

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 105 AN: 284

East Asian (EAS) AF: 0.453 AC: 77 AN: 170

South Asian (SAS) AF: 0.256 AC: 454 AN: 1770

European-Finnish (FIN) AF: 0.450 AC: 191 AN: 424

Middle Eastern (MID) AF: 0.466 AC: 27 AN: 58

European-Non Finnish (NFE) AF: 0.477 AC: 4374 AN: 9164

Other (OTH) AF: 0.481 AC: 403 AN: 838

GnomAD4 genome AF: 0.536 AC: 81525 AN: 152072 Hom.: 22301 Cov.: 32 AF XY: 0.527 AC XY: 39133 AN XY: 74322

African (AFR) AF: 0.594 AC: 24627 AN: 41474

American (AMR) AF: 0.607 AC: 9278 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.432 AC: 1500 AN: 3472

East Asian (EAS) AF: 0.507 AC: 2622 AN: 5172

South Asian (SAS) AF: 0.315 AC: 1517 AN: 4820

European-Finnish (FIN) AF: 0.398 AC: 4208 AN: 10570

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.530 AC: 35991 AN: 67966

Other (OTH) AF: 0.539 AC: 1132 AN: 2102

Alfa AF: 0.482 Hom.: 17148

Bravo AF: 0.562

Asia WGS AF: 0.465 AC: 1617 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.42
DANN	Benign	0.37
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs478304; hg19: chr11-65494260;