rs7757672

chr6-36117548-G-A

Variant summary

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

The XM_047418234.1(MAPK14):c.*1056G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 152,102 control chromosomes in the GnomAD database, including 4,952 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 0.23 (4952 hom., cov: 32)
• Consequence: MAPK14 XM_047418234.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0530

Genes affected

MAPK14 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAPK14	XM_047418234.1	c.*1056G>A		3_prime_UTR_variant	11/11
MAPK14	XM_017010299.3	c.904+1127G>A		intron_variant
MAPK14	XM_017010300.3	c.904+1127G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34449 AN: 151984 Hom.: 4952 Cov.: 32

Gnomad AFR AF: 0.0554

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.0801

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.226 AC: 34441 AN: 152102 Hom.: 4952 Cov.: 32 AF XY: 0.228 AC XY: 16967 AN XY: 74352

Gnomad4 AFR AF: 0.0552

Gnomad4 AMR AF: 0.272

Gnomad4 ASJ AF: 0.260

Gnomad4 EAS AF: 0.0804

Gnomad4 SAS AF: 0.393

Gnomad4 FIN AF: 0.285

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.227

Alfa AF: 0.296 Hom.: 10320

Bravo AF: 0.211

Asia WGS AF: 0.189 AC: 661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	1.9
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7757672; hg19: chr6-36085325;