rs4801824

Variant names:

• chr19-50253873-T-C
• rs4801824
• NM_001145809.2:c.1945+1120T>C

Variant summary

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

The NM_001145809.2(MYH14):​c.1945+1120T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 152,036 control chromosomes in the GnomAD database, including 6,334 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 0.28 (6334 hom., cov: 32)
• Consequence: MYH14 NM_001145809.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.281

Genes affected

MYH14 (HGNC:23212): (myosin heavy chain 14) This gene encodes a member of the myosin superfamily. The protein represents a conventional non-muscle myosin; it should not be confused with the unconventional myosin-14 (MYO14). Myosins are actin-dependent motor proteins with diverse functions including regulation of cytokinesis, cell motility, and cell polarity. Mutations in this gene result in one form of autosomal dominant hearing impairment. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYH14	NM_001145809.2	c.1945+1120T>C		intron_variant	Intron 16 of 42	ENST00000642316.2	NP_001139281.1
MYH14	NM_001077186.2	c.1945+1120T>C		intron_variant	Intron 16 of 41		NP_001070654.1
MYH14	NM_024729.4	c.1921+1120T>C		intron_variant	Intron 15 of 40		NP_079005.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYH14	ENST00000642316.2	c.1945+1120T>C		intron_variant	Intron 16 of 42		NM_001145809.2	ENSP00000493594.1

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43269 AN: 151918 Hom.: 6320 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.285 AC: 43315 AN: 152036 Hom.: 6334 Cov.: 32 AF XY: 0.286 AC XY: 21265 AN XY: 74304

Gnomad4 AFR AF: 0.240

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.307

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.369

Gnomad4 NFE AF: 0.306

Gnomad4 OTH AF: 0.282

Alfa AF: 0.300 Hom.: 9507

Bravo AF: 0.274

Asia WGS AF: 0.299 AC: 1040 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.45

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs4801824; hg19: chr19-50757130;