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GeneBe

rs4988235

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005915(MCM6):c.1917+326C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 151984 control chromosomes in the gnomAD Genomes database, including 17499 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

Frequency

Genomes: 𝑓 0.40 ( 17499 hom., cov: 32)

Consequence

MCM6
NM_005915 intron

Scores

2

Clinical Significance

association no assertion criteria provided O:2

Conservation

PhyloP100: 0.00800

Links

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.56).
BA1
?
GnomAd highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.63 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MCM6NM_005915.6 linkuse as main transcriptc.1917+326C>T intron_variant ENST00000264156.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MCM6ENST00000264156.3 linkuse as main transcriptc.1917+326C>T intron_variant 1 NM_005915.6 P1
MCM6ENST00000483902.1 linkuse as main transcriptn.544+326C>T intron_variant, non_coding_transcript_variant 2
MCM6ENST00000492091.1 linkuse as main transcriptn.343+326C>T intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.397
AC:
60370
AN:
151984
Hom.:
17499
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.121
Gnomad AMI
AF:
0.768
Gnomad AMR
AF:
0.228
Gnomad ASJ
AF:
0.130
Gnomad EAS
AF:
0.00212
Gnomad SAS
AF:
0.163
Gnomad FIN
AF:
0.577
Gnomad MID
AF:
0.0665
Gnomad NFE
AF:
0.635
Gnomad OTH
AF:
0.294
Alfa
AF:
0.505
Hom.:
24250
Bravo
AF:
0.359
Asia WGS
AF:
0.0730
AC:
255
AN:
3478

ClinVar

Significance: association
Submissions summary: Other:2
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Lactase persistence Other:2
association, no assertion criteria providedreference populationiDNA Genomics-- -
association, no assertion criteria providedliterature onlyOMIMJan 26, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.56
Cadd
Benign
11
Dann
Benign
0.91

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs4988235; hg19: chr2-136608646;