chr14-38608194-G-A

Variant names:

• chr14-38608194-G-A
• rs11849174
• ENST00000765620.1:n.91+8740C>T

Variant summary

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

The ENST00000765620.1(ENSG00000299691):​n.91+8740C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 152,044 control chromosomes in the GnomAD database, including 8,683 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 0.34 (8683 hom., cov: 32)
• Consequence: ENSG00000299691 ENST00000765620.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.878
• Publications: 5 publications found

Genes affected

ENSG00000299691 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000765620.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299691	ENST00000765620.1		n.91+8740C>T		intron	N/A
	ENSG00000299691	ENST00000765621.1		n.86+8740C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51202 AN: 151926 Hom.: 8672 Cov.: 32

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.337 AC: 51249 AN: 152044 Hom.: 8683 Cov.: 32 AF XY: 0.341 AC XY: 25298 AN XY: 74286

African (AFR) AF: 0.323 AC: 13400 AN: 41476

American (AMR) AF: 0.335 AC: 5113 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 884 AN: 3470

East Asian (EAS) AF: 0.464 AC: 2400 AN: 5170

South Asian (SAS) AF: 0.408 AC: 1965 AN: 4816

European-Finnish (FIN) AF: 0.378 AC: 3976 AN: 10532

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.331 AC: 22496 AN: 67980

Other (OTH) AF: 0.316 AC: 668 AN: 2112

Alfa AF: 0.329 Hom.: 24145

Bravo AF: 0.335

Asia WGS AF: 0.426 AC: 1479 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.19
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs11849174; hg19: chr14-39077398;